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Wu H, Yang W, Dong G, Hu Q, Li D, Liu J. Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity. HORTICULTURE RESEARCH 2025; 12:uhaf067. [PMID: 40303430 PMCID: PMC12038230 DOI: 10.1093/hr/uhaf067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Accepted: 02/23/2025] [Indexed: 05/02/2025]
Abstract
Kiwifruits, belonging to the genus Actinidia, are acknowledged as one of the most successfully domesticated fruits in the twentieth century. Despite the rich wild resources and diverse phenotypes within this genus, insights into the genomic changes are still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections of Actinidia, leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.0 to 699.6 Mb. By compiling these haplotype genomes, we constructed a super pan-genome for the genus. We identified numerous structural variations (SVs, including variations in gene copy number) and highly diverged regions in these genomes. Notably, significant SV variability was observed within the intronic regions of the MED25 and TTG1 genes across different materials, suggesting their potential roles in influencing fruit size and trichome formation. Intriguingly, our findings indicated a high genetic divergence between two haplotype genomes, with one individual, tentatively named Actinidia × leiocacarpae, from sect. Leiocacarpae. This likely hybrid with a heterozygous genome exhibited notable genetic adaptations related to resistance against bacterial canker, particularly through the upregulation of the RPM1 gene, which contains a specific SV, after infection by Pseudomonas syringae pv. actinidiae. In addition, we also discussed the interlineage hybridizations and taxonomic treatments of the genus Actinidia. Overall, the comprehensive pan-genome constructed here, along with our findings, lays a foundation for examining genetic compositions and markers, particularly those related to SVs, to facilitate hybrid breeding aimed at developing desired phenotypes in kiwifruits.
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Affiliation(s)
- Haolin Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 1st Ring Road, Chengdu, 610065, China
- Department of Urology, Urologic Surgery Center, Xinqiao Hospital, Third Military Medical University (Army Medical University), No. 184 Xinqiao Street, Chongqing, 400037, China
| | - Wenjie Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 1st Ring Road, Chengdu, 610065, China
| | - Guanyong Dong
- Technology Innovation Service Center, No.110 Jiangnan Road, Cangxi, 628400, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 1st Ring Road, Chengdu, 610065, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, No.1 Lumo Road, Wuhan, 430074, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 1st Ring Road, Chengdu, 610065, China
- State Key Laboratory of Grassland AgroEcosystem, College of Ecology, Lanzhou University, No.222 South Tianshui Road, Lanzhou, 730000, China
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2
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She H, Liu Z, Xu Z, Zhang H, Wu J, Wang X, Cheng F, Charlesworth D, Qian W. Genome sequence of the wild species, Spinacia tetrandra, including a phased sequence of the extensive sex-linked region, revealing partial degeneration in evolutionary strata with unusual properties. THE NEW PHYTOLOGIST 2025; 246:2765-2781. [PMID: 40281666 DOI: 10.1111/nph.70165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 04/04/2025] [Indexed: 04/29/2025]
Abstract
Genetic degeneration is a striking feature of Y chromosomes, often involving losses of many genes carried on the X chromosome. However, the time course of gene losses remains unclear. Sex chromosomes of plants evolved more recently than animals' highly degenerated ones, making them ideal for studying degeneration timing. To investigate Spinacia sex chromosome evolution and the time course of degeneration, we compared genome sequences of cultivated Spinacia oleracea, with a small Y-linked region on Chr4, with its two wild relatives. In spinach and its closest relative Spinacia turkestanica, the Y duplication region (YDR) introduced a male-determining factor into Chr4's low-recombining pericentromeric region. In other words, a turnover event occurred in these species' recent common ancestor. The homologous Chr4 of the more distantly related S. tetrandra has a c. 133 Mb completely sex-linked and partially degenerated region, possibly reflecting the ancestral state. Sequence divergence analysis suggests that two 'evolutionary strata' evolved shortly before the two Spinacia lineages split. Consistent with the turnover hypothesis, the YDR of the other two Spinacia species is not within the S. tetrandra older stratum. We discuss the unexpected findings in S. tetrandra that genetic degeneration, genomic rearrangements, and repetitive sequence density are all greatest in the younger stratum.
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Affiliation(s)
- Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyuan Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, 453519, China
| | - Zhaosheng Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Helong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Deborah Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Tu M, Liu N, He Z, Dong X, Gao T, Zhu A, Yang J, Zhang S. Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:2162-2181. [PMID: 40091604 PMCID: PMC12120893 DOI: 10.1111/pbi.70025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 01/20/2025] [Accepted: 02/10/2025] [Indexed: 03/19/2025]
Abstract
Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.
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Affiliation(s)
- Mengling Tu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ningyawen Liu
- University of Chinese Academy of SciencesBeijingChina
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Natural History Museum of Zoology, Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnanChina
| | - Zheng‐Shan He
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Xiu‐Mei Dong
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Tian‐Yang Gao
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Andan Zhu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Jun‐Bo Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Shi‐Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
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4
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Luo J, Luo C, Han M, Wang Q, Song Z, Zhang H, Gao Q, Lin T, Huang C, Zhao Y, Ma C. A natural variation of flavone synthase II gene enhances flavone accumulation and confers drought adaptation in chrysanthemum. THE NEW PHYTOLOGIST 2025. [PMID: 40448392 DOI: 10.1111/nph.70255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Accepted: 05/06/2025] [Indexed: 06/02/2025]
Abstract
Flavones, a key group of flavonoids, play a significant role in plant adaptation to ecological niches and are valuable medicinal resources. However, the genetic basis underlying their contribution to ecological adaptation remains largely unknown. Here, using metabolite-based genome-wide association study, we report that the natural variation of flavone contents in Chrysanthemum indicum, a wild chrysanthemum and medicinal herb, is mainly determined by a recently duplicated flavone synthase II gene CiFNSII-1.2. Enzymatic assays and molecular dynamics simulations reveal that the key amino acid residues 246th and 261th confer the higher enzymatic activity of CiFNSII-1.2 compared with its ancestral form. These residues act as critical modulators, regulating the flexibility of the external entrance and contributing to the enzyme's improved functionality. Transgenic evaluation demonstrate that CiFNSII-1.2 contributes to flavone accumulation and drought adaptation. Our findings provide insights into the biochemical and evolutionary role of flavones in facilitating adaptation to drought-prone habitats in chrysanthemum.
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Affiliation(s)
- Jiayi Luo
- Department of Ornamental Horticulture, College of Horticulture, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Chang Luo
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100092, China
| | - Mingzheng Han
- Department of Ornamental Horticulture, College of Horticulture, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Qinrui Wang
- DP Technology, No. 3 Zhongguancun Street, Beijing, 100089, China
| | - Zhenzhen Song
- Department of Ornamental Horticulture, College of Horticulture, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Haixia Zhang
- Department of Ornamental Horticulture, College of Horticulture, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Qiang Gao
- Qi Biodesign, No. 9 South penglaiyuan Street, Beijing, 102209, China
| | - Tao Lin
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Conglin Huang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100092, China
| | - Yafei Zhao
- Department of Ornamental Horticulture, College of Horticulture, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Chao Ma
- Department of Ornamental Horticulture, College of Horticulture, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
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5
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Wang R, Dai X, Zhao S, Yin Z, Su L, Wang C, Chen H, Zheng L, Liu Y, Zhai Y. Chromosomal-level genome assembly of solitary bee pollinator Osmia excavata Alfken (Hymenoptera: Megachilidae). Sci Data 2025; 12:908. [PMID: 40442156 PMCID: PMC12123002 DOI: 10.1038/s41597-025-05080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Accepted: 04/28/2025] [Indexed: 06/02/2025] Open
Abstract
Osmia spp. is a genus of solitary bees that serves as excellent pollinators for various fruit trees and has the potential to enhance pollination services in both agricultural and natural ecosystems. However, the absence of high-quality genomic resources limits our insights into evolutionary biology and ecological adaptations of Osmia. Here, we present a chromosome-level genome of Osmia excavata, using PacBio, Illumina, and Hi-C data. The genome has a total size of 164.35 Mb, with a scaffold N50 of 9.81 Mb, and the majority of contigs (98.50%, 161.88 Mb) are organized into sixteen chromosomes. BUSCO analysis reveals a completeness score of 99.7% (n = 1,367), with 99.6% identified as single-copy BUSCOs and 0.1% as duplicated BUSCOs. The genome contains 13.46% (22.11 Mb) repetitive elements and encodes 11,452 predicted protein-coding genes. This study provides a crucial genomic resource for our understanding of solitary bees' evolution and ecological roles.
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Affiliation(s)
- Ruijuan Wang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China
| | - Xiaoyan Dai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China
| | - Shan Zhao
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China
| | - Zhenjuan Yin
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Long Su
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China
| | - Chengxing Wang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China
| | - Hao Chen
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China
| | - Yan Liu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China.
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China.
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China.
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Shandong Key Laboratory for Green Prevention and Control of Agricultural Pests, Jinan, 250100, China.
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China.
- Shandong Engineering Research Center of Resource Insects, Jinan, 250100, China.
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Sun D, Lv J, Gao B, Jia S, Liu P, Li J, Li J, Ren X. Chromosome-level genome assembly of scalloped spiny lobster Panulirus homarus homarus. Sci Data 2025; 12:900. [PMID: 40436891 PMCID: PMC12120130 DOI: 10.1038/s41597-025-05253-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 05/21/2025] [Indexed: 06/01/2025] Open
Abstract
Lobsters, aquatic organisms of significant economic value, hold an important position in the global aquaculture and fisheries industries. However, due to overfishing and ecological change, the populations of certain lobster species have declined dramatically, prompting conservation efforts in various countries. However, limited genomics research has restricted our capacity to conserve and exploit lobster germplasm resources. Here, we present a chromosome-level reference genome for Panulirus homarus homarus constructed using PacBio long-read sequencing and Hi-C data. The genome assembly size was 2.61 Gb, with a contig N50 of 5.43 Mb, and a scaffold N50 of 36.69 Mb. The assembled sequences were anchored to 73 chromosomes, covering 96.05% of the total genome. A total of 25,580 protein-coding genes were predicted, and 99.98% of the genes were functionally annotated using various protein databases. The high-quality genome assembly provides a valuable resource for studying the biology and evolutionary history of P. h. homarus, and could facilitate sustainable resource management, aquaculture, and conservation of the species.
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Affiliation(s)
- Dongfang Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Jianjian Lv
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Baoquan Gao
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Shaoting Jia
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Ping Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Jian Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China
| | - Jitao Li
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China.
| | - Xianyun Ren
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, Shandong, 266237, China.
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7
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Wei Z, Li Y, Li Y, Liu J, Ding S, Chen X, Shi A, Yang D. Chromosome-level genome assembly of Sambus kanssuensis (Coleoptera: Buprestidae). Sci Data 2025; 12:895. [PMID: 40436974 PMCID: PMC12119912 DOI: 10.1038/s41597-025-05271-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Accepted: 05/21/2025] [Indexed: 06/01/2025] Open
Abstract
Sambus kanssuensis Ganglbauer, 1890 (Coleoptera: Buprestidae), distributed in Gansu and Sichuan Provinces of China, is a phytophagous pest that feeds on the toxic plant Buddleja. However, the genomic resources of this beetle remain unknown, which impedes the understanding of its ecological adaptations. Consequently, this study presents a complete, well-assembled, and annotated genome of S. kanssuensis. The assembled results indicate a genome size of 312.42 Mb, comprising 206 scaffolds, with an N50 of 34.04 Mb; 98.68% of the assembly sequences were anchored to 11 chromosomes, including one sex chromosome. The genome contains 12,723 protein-coding genes, of which 11,977 have been annotated. BUSCO analysis revealed that the completeness of the chromosome-level genome is 97.9%. This chromosome-level genome provides valuable data for further investigations into detoxification mechanisms, ecological adaptations, population genetics, and the evolution of Buprestidae.
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Affiliation(s)
- Zhonghua Wei
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
- State Key Laboratory of Green Pesticides, Guizhou University, Guiyang, Guizhou, 550025, China
- State Key Laboratory of Agricultural and Forestry Biosecurity, MARA Key Lab of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Yunchun Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Yingying Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Jiuzhou Liu
- State Key Laboratory of Agricultural and Forestry Biosecurity, MARA Key Lab of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Shuangmei Ding
- The Institute of Scientific and Technical Research on Archives, National Archives Administration of China, Beijing, 100050, China
| | - Xulong Chen
- State Key Laboratory of Green Pesticides, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Aimin Shi
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
| | - Ding Yang
- State Key Laboratory of Green Pesticides, Guizhou University, Guiyang, Guizhou, 550025, China.
- State Key Laboratory of Agricultural and Forestry Biosecurity, MARA Key Lab of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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8
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Yan Z, Shi X, Cai Y, Sun W, He P, Wu L, Zhang J, Guo X, Wang B, Yu F, Liu W. Chromosome-level genome assemblies of Verpa bohemica and Verpa conica. Sci Data 2025; 12:880. [PMID: 40425600 PMCID: PMC12117090 DOI: 10.1038/s41597-025-05224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Accepted: 05/16/2025] [Indexed: 05/29/2025] Open
Abstract
Verpa, commonly known as "early morel" or "false morel", plays an important ecological role and offers considerable economic and medicinal potential. Despite their significance, research on Verpa species, particularly V. bohemica and V. conica, remains limited. In this study, we assembled high-quality sub-chromosomal genomes of six Verpa strains using Nanopore and Illumina sequencing, with average sizes of 44.38 Mb for V. bohemica and 45.40 Mb for V. conica. Specifically, the assemblies of V. bohemica strain 21108 and V. conica strain 21120 were anchored to 26 and 25 chromosomes with Hi-C technologies, respectively. The consensus quality value (QV) of both V. bohemica and V. conica exceeded 40. In addition, an average of 11,024 and 11,052 protein-coding genes were identified for V. bohemica and V. conica, respectively, with BUSCO completeness scores ranging from 98.71% to 99.24%. Overall, these reported genomes will provide valuable genomic resources for the evolution and ecological roles research of Verpa.
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Affiliation(s)
- Zhuyue Yan
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, School of Ethnic Medicine, Yunnan Minzu University Kunming, Kunming, 650500, China
| | - Yingli Cai
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, School of Ethnic Medicine, Yunnan Minzu University Kunming, Kunming, 650500, China
| | - Wenhua Sun
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Peixin He
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China
| | - Liyuan Wu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jin Zhang
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xing Guo
- Yichun Branch of Heilongjiang Academy of Forestry Sciences, Yichun, 153000, China
| | - Bo Wang
- Gansu Province Xiaolong mountains forestry protect center's Dangchuan forest farm, Tianshui, 741020, China
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Wei Liu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, School of Ethnic Medicine, Yunnan Minzu University Kunming, Kunming, 650500, China.
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9
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Ding Y, Zhao Y, Xie Y, Wang F, Bi W, Wu M, Zhao G, Gong Y, Li W, Zhang P. High-quality assembly of the chromosomal genome for Flemingia macrophylla reveals genomic structural characteristics. BMC Genomics 2025; 26:535. [PMID: 40419955 DOI: 10.1186/s12864-025-11705-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 05/13/2025] [Indexed: 05/28/2025] Open
Abstract
Flemingia macrophylla, a prominent shrub species within the Fabaceae family, is widely distributed across China and Southeast Asia. In addition to its ecological importance, it possesses notable medicinal value, with its roots traditionally used for treating rheumatism, enhancing blood circulation, and alleviating joint pain. We employed Nanopore sequencing platforms to generate a high-quality reference genome for F. macrophylla, with an assembled genome size of 1.01 Gb and a contig N50 of 59.43 Mb. A total of 33,077 protein-coding genes were predicted, and BUSCO analysis indicated a genome completeness of 99%. Phylogenomic analyses showed that F. macrophylla is most closely related to Cajanus cajan among the sampled taxa, with an estimated divergence time of 13.2-20.0 MYA. Evidence of whole-genome duplication (WGD) events was detected in F. macrophylla, C. cajan, and P. vulgaris, with these species sharing two WGD events. The unique gene families in F. macrophylla are associated with strong resistance to both abiotic and biotic stress, supporting its remarkable ecological adaptability. Furthermore, gene family expansion analysis revealed a significant enrichment of genes related to secondary metabolites biosynthesis, providing a molecular basis for its high medicinal value. In summary, this study provides a foundational genomic resource for F. macrophylla, offering valuable insights into its genetic architecture, evolutionary history, and potential applications in medecine and agriculture. The comprehensive analyses lay the groundwork for future research into the species's medicinal properties and evolutionary biology.
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Affiliation(s)
- Ye Ding
- Department of Chinese Materia Medica, Hunan Institute for Drug Control, Changsha, Hunan, 410001, P. R. China
| | - Yi Zhao
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou, Zhuzhou, Hunan, 412000, P. R. China
| | - Yangqin Xie
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei, 430000, P. R. China
| | - Fan Wang
- Wuhan Benagen Technology Co., Ltd, Wuhan, Hubei, 430000, P. R. China
| | - Wu Bi
- Department of Chinese Materia Medica, Hunan Institute for Drug Control, Changsha, Hunan, 410001, P. R. China
| | - Mengyao Wu
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou, Zhuzhou, Hunan, 412000, P. R. China
| | - Guilin Zhao
- Department of Chinese Materia Medica, Hunan Institute for Drug Control, Changsha, Hunan, 410001, P. R. China
| | - Yun Gong
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou, Zhuzhou, Hunan, 412000, P. R. China
| | - Wenli Li
- Department of Chinese Materia Medica, Hunan Institute for Drug Control, Changsha, Hunan, 410001, P. R. China
| | - Peng Zhang
- Zhuzhou Qianjin Pharmaceutical Co., Ltd. Zhuzhou, Zhuzhou, Hunan, 412000, P. R. China.
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10
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Wang LY, Xiao L, Ren TY, Cheng LX, Xiong JH, Fan Z, Zhang ZS. A chromosomal-level genome assembly of Araneus marmoreus Schenkel, 1953 (Araneae: Araneidae). Sci Data 2025; 12:859. [PMID: 40413234 PMCID: PMC12103598 DOI: 10.1038/s41597-025-05215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Accepted: 05/15/2025] [Indexed: 05/27/2025] Open
Abstract
The marbled orb-weaver spider, Araneus marmoreus (Araneae: Araneidae), is distinguished by its unique inflated, pumpkin-like abdomen. Numerous genome studies have been conducted on Araneidae species, providing insights into their unique biological traits. However, studies on A. marmoreus remain limited, despite its ecological significance and intriguing morphology. The lack of a high-quality reference genome has further hindered in-depth exploration of its evolutionary biology and ecological dynamics. Here, we present a chromosome-level genome assembly for A. marmoreus, generated using a combination of Illumina, PacBio, and Hi-C sequencing technologies. The assembled genome is 2.39 Gb in size, comprising 13 chromosomes, with a scaffold N50 of 181.8 Mb and a contig N50 of 721.3 kb. The assembly achieved a BUSCO completeness score of 97.1% (n = 2,934), including 91.0% complete and single-copy BUSCOs and 6.1% complete and duplicated BUSCOs. Repetitive sequences accounted for 59.25% of the genome, and 23,381 protein-coding genes were annotated. This high-quality genome provides a valuable resource for advancing research into the evolutionary genomics and ecological dynamics of A. marmoreus.
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Affiliation(s)
- Lu-Yu Wang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Lin Xiao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Tian-Yu Ren
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Ling-Xin Cheng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jun-Han Xiong
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zheng Fan
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China.
| | - Zhi-Sheng Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China.
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11
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Ning Y, Li Y, Li CY, Wang JZ, Wang TS, Zheng YC, Zhan YY, Xu SJ, Dong SB, Wang YF. Chromosome-level genome assembly for clubrush (Scirpus × mariqueter) endemic to China. Sci Data 2025; 12:839. [PMID: 40404652 PMCID: PMC12098773 DOI: 10.1038/s41597-025-05204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Accepted: 05/14/2025] [Indexed: 05/24/2025] Open
Abstract
Scirpus × mariqueter (Tang & F.T.Wang) Tatanov, which is endemic to eastern estuaries in China, is a tidal zone-engineering species with great promise for managing greenhouse gases and enhancing ecosystem resilience against invasive species. Although S. mariqueter is widely recognized as a hybrid species derived from Bolboschoenus planiculmis (F. Schmidt) T.V. Egorova and Schoenoplectus triqueter (L.) Palla, its speciation remains highly controversial. The lack of a reference genome is the major cause of this ambiguity. We generated the first chromosome-level genome assembly for S. mariqueter combining PacBio long-reads, Illumina short-reads, and the Hi-C method. The genome assembly consisted of 227.75 Mb (contig N50: 3.89 Mb). We also constructed a haploid karyotype comprising 54 pseudochromosomes. The average size of these pseudochromosomes was small (4.05 Mb). Thirty-two pseudochromosomes were assembled to a telomere to telomere level. Repetitive elements represented approximately 54.12% of the genome. We predicted and annotated 25,239 protein-coding genes. The overall BUSCO score was 95.10%, with notably few duplicated genes (1.70%). This high-quality genome provides critical data for future studies.
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Affiliation(s)
- Yu Ning
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Yang Li
- Huzhou University, Huzhou, China
| | - Chun Yi Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China.
| | - Jin Zhi Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Tian Shi Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Yan Chao Zheng
- East China Inventory and Planning Institute, Hangzhou, China
| | - Yang Ying Zhan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Shen Jian Xu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Shu Bin Dong
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Fei Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- State Key Laboratory of Wetland Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
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12
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Liu Y, Li X, Meng Y, Wu Y, Jin Y, Ma X, Zhou W, Tan Y, Lin FC, Wang H. The whole genome sequence of Cordyceps cicadae - an edible and potential medicinal fungus. Mol Genet Genomics 2025; 300:50. [PMID: 40399565 DOI: 10.1007/s00438-025-02255-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 04/24/2025] [Indexed: 05/23/2025]
Abstract
Cordyceps cicadae is an entomopathogenic fungus from the Cordyceps genus and a well-known edible mushroom with a long history of use in Asia. It contains many bioactive compounds beneficial to human health, giving it broad application prospects in medicine. In this study, we generated the complete genome sequence of C. cicadae strain 2-2 using a combination of Illumina, PacBio, and Hi-C sequencing technologies. This comprehensive genome sequence comprises 9 chromosomes, an N50 contig size of 4,798,690 bp, a GC content ratio of 52.65%, a total size of 34.60 Mb, and 8,019 predicted coding genes. Additionally, we conducted functional annotation of the genome, revealing that 63.2% of the genes were enriched in 50 GO terms and 87.8% in 387 KEGG pathways. We also identified 542 enzyme genes, noting that C. cicadae has a greater number of GHs compared to other fungi in the Cordyceps genus. Notably, NR database analysis revealed that 6,441 genes in C. cicadae are similar to those in Cordyceps fumosorosea, suggesting that C. cicadae may serve as a cost-effective alternative to this expensive traditional medicinal fungus. This study presents the first chromosome-level genome of the Cordyceps genus, providing a comprehensive analysis of the genetic composition and functions of C. cicadae and establishing a foundation for advancing research and development of Cordyceps fungi.
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Affiliation(s)
- Yuwei Liu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueqian Li
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiqi Meng
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yifan Wu
- School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yuting Jin
- Chengde Medical University, Chengde, Hebei, 067000, The People's Republic of China
| | - Xiaotong Ma
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wei Zhou
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuchong Tan
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fu-Cheng Lin
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro- Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongkai Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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13
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Ito Y, Sanno R, Ashikari S, Yura K, Asahi T, Ylla G, Kataoka K. Chromosome-scale whole genome assembly and annotation of the Jamaican field cricket Gryllus assimilis. Sci Data 2025; 12:826. [PMID: 40394066 PMCID: PMC12092778 DOI: 10.1038/s41597-025-05197-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Accepted: 05/14/2025] [Indexed: 05/22/2025] Open
Abstract
Gryllus assimilis, commonly known as Jamaican field cricket, is an edible insect with significant economic value in sustainable food production. Despite its importance, a high-quality reference genome of G. assimilis has not yet been published. Here, we report a chromosome-level reference genome of G. assimilis based on Oxford Nanopore Technologies (ONT) sequencing, Illumina sequencing, and Hi-C technologies. The assembled genome has a total length of 1.60 Gbp with a scaffold N50 of 102 Mbp, and 96.80% of the nucleotides was assigned to 15 chromosome-scale scaffolds. The assembly completeness was validated using BUSCO, achieving 99.5% completeness against the arthropoda database. We predicted 27,645 protein-coding genes, and 825 Mb repetitive elements were annotated in the reference genome. This reference genome of G. assimilis can provide a basis for the subsequent development of genomic resources, offering insights for future functional genomic studies, comparative genomics, and DNA-informed breeding of this species.
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Affiliation(s)
- Yuki Ito
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | | | - Kei Yura
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Guillem Ylla
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
- Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan.
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14
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Li Q, He K, Lu Y, He B, Zheng X, Lu Z, Li F, Xu H. A vetiver-specific terpene synthase VzTPS9 contributes to the high attractiveness of vetiver to rice stem borer. Proc Natl Acad Sci U S A 2025; 122:e2424863122. [PMID: 40324074 DOI: 10.1073/pnas.2424863122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 03/27/2025] [Indexed: 05/07/2025] Open
Abstract
Vetiver (Vetiveria zizanioides) is highly attractive to the rice stem borer (Chilo suppressalis, RSB) and is widely utilized as a trap plant for RSB control in East Asia. However, the underlying mechanism driving this high level of attractiveness remains unclear. In this study, we identified volatiles emitted by vetiver using SPME/GC-MS and found that cedrol constitutes 12.15% of the total volatile profile. Both Y-tube olfactometer and electroantennography assays revealed that cedrol is highly attractive to female RSB moths at a concentration of 200 μg/μL. To investigate the mechanism responsible for the high level of cedrol in vetiver, we sequenced and assembled a chromosome-level genome of vetiver, identifying a vetiver-specific terpene synthase, VzTPS9, which is responsible for the synthesis of cedrol from farnesyl pyrophosphate (FPP). Subsequently, we constructed a transgenic rice line by integrating VzTPS9 into the rice genome. Enzyme assays and gene expression analyses demonstrated that the transgenic rice produced higher levels of cedrol, which were positively correlated with VzTPS9 expression levels, and consequently, with increased attractiveness to female RSB moths. These findings suggest that increased expression of VzTPS9 in vetiver leads to elevated cedrol synthesis, contributing to its enhanced attractiveness to RSB. This work uncovers the molecular mechanism behind vetiver's high attractiveness to RSB and provides valuable insights for developing more effective strategies for utilizing vetiver as a trap plant in RSB control.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310021, China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Kang He
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310021, China
| | - Yanhui Lu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Bingbing He
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310021, China
| | - Xusong Zheng
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhongxian Lu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310021, China
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Hongxing Xu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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15
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Martinez-Hernandez JE, Salvo-Garrido H, Levicoy D, Caligari PDS, Rupayán A, Moyano T, Carrasco M, Hernandez S, Armijo-Godoy G, Westermeyer F, Larama G. Genomic structure of yellow lupin (Lupinus luteus): genome organization, evolution, gene family expansion, metabolites and protein synthesis. BMC Genomics 2025; 26:477. [PMID: 40369454 PMCID: PMC12076967 DOI: 10.1186/s12864-025-11678-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 05/06/2025] [Indexed: 05/16/2025] Open
Abstract
Yellow lupin (Lupinus luteus) gives valuable high-quality protein and has good sustainability due to its ability in nitrogen fixation and exudation of organic acids, which reduces the need for chemical-based phosphate fertilization in acid soils. However, the crop needs further improvements to contribute in a major way to sustainable agriculture and food security.In this study, we present the first chromosome-level genome assembly of L. luteus. The results provide insights into its genomic organization, evolution, and functional attributes. Using integrated genomic approaches, we unveil the genetic bases governing its adaptive responses to environmental stress, delineating the intricate interplay among alkaloid biosynthesis, mechanisms of pathogen resistance, and secondary metabolite transporters. Our comparative genomic analysis of closely related species highlights recent speciation events within the Lupinus genus, exposing extensive synteny preservation alongside notable structural alterations, particularly chromosome translocations. Remarkable expansions of gene families implicated in terpene metabolism, stress responses, and conglutin proteins were identified, elucidating the genetic basis of L. luteus' superior nutritional profile and defensive capabilities. Additionally, a diverse array of disease resistance-related (R) genes was uncovered, alongside the characterization of pivotal enzymes governing quinolizidine alkaloid biosynthesis, thus shedding light on the molecular mechanisms underlying "bitterness" in lupin seeds.This comprehensive genomic analysis serves as a valuable resource to improve this species in terms of resilience, yield, and seed protein levels to contribute to food and feed to face the worldwide challenge of sustainable agriculture and food security.
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Affiliation(s)
- J Eduardo Martinez-Hernandez
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de Las Américas, Santiago, 7500975, Chile
| | - Haroldo Salvo-Garrido
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile.
| | - Daniela Levicoy
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
| | - Peter D S Caligari
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
| | - Annally Rupayán
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Makarena Carrasco
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
| | - Sebastián Hernandez
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
| | - Grace Armijo-Godoy
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
| | - Fernando Westermeyer
- CGNA (Agriaquaculture Nutritional Genomic Center), Las Heras 350, Temuco, 4781158, Chile
| | - Giovanni Larama
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, 4811230, Chile
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16
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Yu H, Guo J, Wu X, Liang J, Fan S, Du H, Zhao S, Li Z, Liu G, Xiao Y, Luo J, Gao Y, Chen Q, Gao H, Peng F. Haplotype-resolved genome assembly provides insights into the genetic basis of green peach aphid resistance in peach. Curr Biol 2025:S0960-9822(25)00556-1. [PMID: 40381617 DOI: 10.1016/j.cub.2025.04.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 03/06/2025] [Accepted: 04/23/2025] [Indexed: 05/20/2025]
Abstract
Green peach aphid (GPA) is one of the most destructive pests of peach, threatening both growth and fruit quality. However, the mechanism underlying GPA resistance remains unclear. Here, we performed haplotype-resolved genome assembly of a GPA-resistant cultivar and identified an allele-specific expressed gene, PpNLR1, responsible for the GPA-resistant trait. A genome-wide association study (GWAS) revealed a functional 20-bp insertion or deletion (indel) in the PpNLR1 promoter, which co-segregated with the GPA-resistant trait and directly influenced promoter activity. Furthermore, jasmonate (JA) signaling, activated during GPA infestation, induced the transcription of PpERF109. This transcription factor specifically bound to the "CAAGT" motif within the GWAS-identified 20-bp insertion of the PpNLR1 promoter, resulting in allele-specific expression (ASE). Functional validation of the two alleles (PpNLR1-Hap1 and PpNLR1-Hap2) in both peach and Arabidopsis demonstrated their role in aphid resistance. Additionally, two GPA salivary proteins were identified as effectors, triggering reactive oxygen species (ROS) and activating the peach immune system in conjunction with the PpNLR1 protein. Comparative genomics and phylogenetic analysis indicated that an ∼53.6-kb genomic variation surrounding PpNLR1 underwent negative selection during peach evolution. In conclusion, the JA-mediated PpERF109-PpNLR1 module and GPA effector proteins significantly contribute to GPA resistance in peach. The novel haplotype-resolved genome assembly and identified key genes provide valuable resources for future genomic research and GPA resistance breeding in peach.
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Affiliation(s)
- Haixiang Yu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Jian Guo
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China.
| | - Xuelian Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Jiahui Liang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Shihao Fan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Hao Du
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Shilong Zhao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Zhaoyang Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Guangyuan Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Yuansong Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Jingjing Luo
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Yangyang Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Qiuju Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Huaifeng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Futian Peng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China.
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17
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Liu Y, Chen Y, Ren Z, Li K, Wang X, Wu K, Liu J, Sade N, He H, Li S, Jiang H, Han X. Two haplotype-resolved telomere-to-telomere genome assemblies of Xanthoceras sorbifolium. Sci Data 2025; 12:791. [PMID: 40368912 PMCID: PMC12078709 DOI: 10.1038/s41597-025-05057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Accepted: 04/23/2025] [Indexed: 05/16/2025] Open
Abstract
Yellowhorn (Xanthoceras sorbifolium) is widely used in northern China for landscaping, desertification control, and oil production. However, the lack of high-quality genomes has hindered breeding and evolutionary studies. Here, we present the first haplotype-resolved, telomere-to-telomere (T2T) yellowhorn genomes of PBN-43 (white single-flowered) and PBN-126 (white double-flowered) using PacBio HiFi and Hi-C data. These assemblies range from 464.34 Mb to 468.97 Mb and include all centromeres and telomeres. Genome annotation revealed that an average of 67.99% (317.09 Mb) of yellowhorn genomic regions consist of repetitive elements across all haplotypes. The number of protein-coding genes ranges from 35,039 to 35,174 among assemblies, representing an average 50.16% increase over the first published yellowhorn genome. Additionally, 93.90% of the annotated genes have functional annotations. We found yellowhorn experienced an LTR-RT burst during the last 0.45-0.48 Mya. These data provide a resource for investigating genomic variations, phylogenetic relationships, duplication modes, and the distribution of nucleotide-binding leucine-rich repeat (NLR) genes, and support further research into yellowhorn breeding.
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Affiliation(s)
- Yu Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
| | - Yijun Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Zizheng Ren
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
| | - Kui Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
| | - Xu Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
| | - Kai Wu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
| | - Jinfeng Liu
- Shandong Woqi Agriculture Development Co., Ltd, Weifang, 262100, China
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Shouke Li
- Shandong Woqi Agriculture Development Co., Ltd, Weifang, 262100, China.
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Xue Han
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China.
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18
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DeWeese K, Molano G, Calhoun S, Lipzen A, Jenkins J, Williams M, Plott C, Talag J, Grimwood J, Jannink JL, Grigoriev IV, Schmutz J, Yarish C, Nuzhdin S, Lindell S. Scaffolded and annotated nuclear and organelle genomes of the North American brown alga Saccharina latissima. Front Genet 2025; 16:1494480. [PMID: 40438323 PMCID: PMC12116465 DOI: 10.3389/fgene.2025.1494480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 04/23/2025] [Indexed: 06/01/2025] Open
Abstract
Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica. While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.
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Affiliation(s)
- Kelly DeWeese
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States
| | - Gary Molano
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Jean-Luc Jannink
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Ithaca, NY, United States
- Section On Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Charles Yarish
- Department of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, United States
- Applied Ocean Physics and Engineering Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Sergey Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States
| | - Scott Lindell
- Department of Ecology and Evolutionary Biology, University of Connecticut, Stamford, CT, United States
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19
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Wu B, Luo D, Yue Y, Yan H, He M, Ma X, Zhao B, Xu B, Zhu J, Wang J, Jia J, Sun M, Xie Z, Wang X, Huang L. New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis. Genome Biol 2025; 26:128. [PMID: 40369670 PMCID: PMC12076936 DOI: 10.1186/s13059-025-03604-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 05/06/2025] [Indexed: 05/16/2025] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear. RESULTS Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region. CONCLUSIONS Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.
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Affiliation(s)
- Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuesen Yue
- Institute of Grassland, Flower and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xixi Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bingyu Zhao
- College of Agriculture and Life Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Zhu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610061, China
| | - Jiyuan Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Advanced Study, Chengdu University, Chengdu, 610106, China
| | - Zheni Xie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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20
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Wang J, Chen K, Zhang R, Huang Y, Chen J. A haplotype-resolved genome assembly and gene expression map of Cushion willow. Sci Data 2025; 12:785. [PMID: 40360525 PMCID: PMC12075806 DOI: 10.1038/s41597-025-05132-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 05/01/2025] [Indexed: 05/15/2025] Open
Abstract
Salix brachista, commonly known as Cushion willow, is a common component of subnival alpine assemblages and a dioecious or monoecious plant with a creeping stem and numerous lateral branches. Cushion willow takes cuttings more easier and has a specific sex system, making it a suitable system for studying the evolution of plant sex determination, adaptive evolution of alpine plants, and mining stress resistance gene resource that cope with the hostile alpine environment. Therefore, Cushion willow has potential value in genetic improvements for willows used as bioenergy crops, in gardening, and as ornamental plants. However, the genome of Cushion willow still contains some un-assembled repetitive sequences, and there is limited availability of a gene expression atlas, which hinders its potential use for the aforementioned purposes. Here, we updated the genome of Cushion willow to be haplotype-resolved and near telomere-to-telomere, and obtained a high-quality transcriptomic map. Our research provides a potential model species for alpine adaptive research, sex determination evolution studies, and improving willow crops.
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Affiliation(s)
- Jindan Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Kaiyun Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, P. R. China
| | - Rengang Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, 650092, Yunnan, P. R. China.
| | - Jiahui Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, P. R. China.
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21
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Han X, Li X, Xu L, Liu Q, Su S, Yao W, He W. The telomere-to-telomere genome assembly and annotation of the rock carp (Procypris rabaudi). Sci Data 2025; 12:781. [PMID: 40360522 PMCID: PMC12075466 DOI: 10.1038/s41597-025-05066-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Accepted: 04/24/2025] [Indexed: 05/15/2025] Open
Abstract
Procypris rabaudi, commonly known as the rock carp, is an endemic economic fish in the middle-upper reaches of the Yangtze River. To enhance the understanding the biology of rack carps, a high-quality reference genome is required in different areas of study. Here, we generated the first telomere-to-telomere genome assembly and annotation of the rock carp, which spans 1.64 Gb with a contig N50 of 32.36 Mb. Hi-C assembly suggested that 99.83% sequences were positioned to 50 pseudo-chromosomes. Notably, 43 chromosomes were assembled without any gap. Through the integration of homologous-based predictions and RNA-sequencing technology, we identified 44,402 protein-coding genes, with 43,663 of them (98.3%) predicted to be functional. Furthermore, our assembled genome achieved 98.1% BUSCO completeness. This work improves the quality of the rock carp genome and provides valuable foundation for the future studies of genomics, biology and the fishery resources breeding.
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Affiliation(s)
- Xiaolu Han
- College of Fisheries, Southwest University, Chongqing, 400715, China
| | - Xinle Li
- College of Fisheries, Southwest University, Chongqing, 400715, China
| | - Luohao Xu
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qi Liu
- Wuhan Onemore-tech Co. Ltd, Wuhan, Hubei, 430076, China
| | - Shengqi Su
- College of Fisheries, Southwest University, Chongqing, 400715, China
| | - Weizhi Yao
- College of Fisheries, Southwest University, Chongqing, 400715, China
| | - Wenping He
- College of Fisheries, Southwest University, Chongqing, 400715, China.
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22
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Chen P, Zhong Z, Jin WX, Sun J, Sun SC. Chromosome-scale assembly of Artemia tibetiana genome, first aquatic invertebrate genome from Tibet Plateau. Sci Data 2025; 12:777. [PMID: 40355476 PMCID: PMC12069563 DOI: 10.1038/s41597-025-05136-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 05/01/2025] [Indexed: 05/14/2025] Open
Abstract
Genomic-level studies on the adaptive evolution of animals in the Qinghai-Tibet Plateau have been rapidly increasing. However, most studies are concentrated on vertebrates, and there are few reports on invertebrates. Here, we report the chromosome-level genome assembly for the brine shrimp Artemia tibetiana from Kyêbxang Co, a high-altitude (4620 m above sea level) salt lake on the plateau, based on the combination of Illumina, Nanopore long-reads and Hi-C sequencing data. The assembled genome is 1.69 Gb, and 94.83% of the assembled sequences are anchored to 21 pseudo-chromosomes. Approximately 75% of the genome was identified as repetitive sequences, which is higher than most crustaceans documented so far. A total of 17,988 protein-coding genes were identified, among them 14,388 were functionally annotated. This genomic resource provides the foundation for whole-genome level investigation on the genetic adaptation of Artemia to the harsh conditions in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Panpan Chen
- Fisheries College, Ocean University of China, Qingdao, 266000, China
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China
| | - Zhaoyan Zhong
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China
| | - Wei-Xin Jin
- Fisheries College, Ocean University of China, Qingdao, 266000, China
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China
| | - Jin Sun
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China.
| | - Shi-Chun Sun
- Fisheries College, Ocean University of China, Qingdao, 266000, China.
- MOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266000, China.
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23
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Liu S, Shi C, Chen C, Tan Y, Tian Y, Macqueen DJ, Li Q. Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves. Cell Rep 2025; 44:115697. [PMID: 40349337 DOI: 10.1016/j.celrep.2025.115697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 03/20/2025] [Accepted: 04/23/2025] [Indexed: 05/14/2025] Open
Abstract
Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade, we show that despite genome size reduction during evolution, these bivalves maintain remarkable genetic variability. By constructing a haplotype-resolved genome for Crassostrea sikamea, we identify widespread haplotype divergent sequences (HDSs), representing genomic regions unique to each haplotype. We show that HDSs are driven by transposable elements, playing a key role in creating and maintaining genetic diversity during oyster evolution. Comparisons of haplotype-resolved genomes across four bivalve orders uncover diverse HDS origins, highlighting a role in genetic innovation and expression regulation across broad timescales. Further analyses show that, in oysters, haplotype polymorphisms drive gene expression variation, which is likely to promote phenotypic plasticity and adaptation. These findings advance our understanding of the relationships among genome structure, diversity, and adaptability in a highly successful invertebrate group.
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Affiliation(s)
- Shikai Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China.
| | - Chenyu Shi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Chenguang Chen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Ying Tan
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Yuan Tian
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, China.
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24
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Susek K, Vincenzi L, Tomaszewska M, Kroc M, Franco E, Cosentino E, Limongi AR, Tanwar UK, Jamil H, Nelson MN, Bayer PE, Edwards D, Papa R, Delledonne M, Jackson SA. The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution. Nat Commun 2025; 16:4358. [PMID: 40348738 PMCID: PMC12065815 DOI: 10.1038/s41467-025-58531-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/20/2025] [Indexed: 05/14/2025] Open
Abstract
Lupin crops provide nutritious seeds as an excellent source of dietary protein. However, extensive genomic resources are needed for crop improvement, focusing on key traits such as nutritional value and climate resiliency, to ensure global food security based on sustainable and healthy diets for all. Such resources can be derived either from related lupin species or crop wild relatives, which represent a large and untapped source of genetic variation for crop improvement. Here, we report genome assemblies of the cross-compatible species Lupinus cosentinii (Mediterranean) and its pan-Saharan wild relative L. digitatus, which are well adapted to drought-prone environments and partially domesticated. We show that both species are tetraploids, and their repetitive DNA content differs considerably from that of the main lupin crops L. angustifolius and L. albus. We present the complex evolutionary process within the rough-seeded lupins as a species-based model involving polyploidization and rediploidization. Our data also provide the foundation for a systematic analysis of genomic diversity among lupin species to promote their exploitation for crop improvement and sustainable agriculture.
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Affiliation(s)
- Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland.
| | - Leonardo Vincenzi
- Functional Genomics Lab, Department of Biotechnology, University of Verona, Verona, Italy
| | - Magdalena Tomaszewska
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Kroc
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Edoardo Franco
- Functional Genomics Lab, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Antonina Rita Limongi
- Functional Genomics Lab, Department of Biotechnology, University of Verona, Verona, Italy
| | - Umesh Kumar Tanwar
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Humaira Jamil
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Matthew Nicholas Nelson
- Floreat Laboratories, The Commonwealth Scientific and Industrial Research Organisation, Floreat, WA, Australia
| | - Philipp E Bayer
- OceanOmics, The Minderoo Foundation, Perth, WA, Australia
- The UWA Oceans Institute, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- Centre for Applied Bioinformatics and School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Massimo Delledonne
- Functional Genomics Lab, Department of Biotechnology, University of Verona, Verona, Italy
- Genartis srl, Via Albere 17, 37138, Verona, Italy
| | - Scott A Jackson
- Institute for Plant Breeding and Genetics, University of Georgia, Athens, GA, USA
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25
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Kon T, Kon-Nanjo K, Handayani KS, Zang L, Fahrurrozi F, Simakov O, Gultom VDN, Shimada Y. Chromosome-level genome assembly of the doctor fish (Garra rufa). Sci Data 2025; 12:765. [PMID: 40346083 PMCID: PMC12064734 DOI: 10.1038/s41597-025-05101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2025] [Accepted: 04/29/2025] [Indexed: 05/11/2025] Open
Abstract
Garra rufa, or doctor fish, is a small cyprinid known for its high-temperature tolerance and its use in ichthyotherapy. Recently, this trait has gained interest as a model for human diseases, including infections and cancer xenografts, though limited genomic resources hinder experimental use. In this study, we have generated a high-quality, chromosome-level genome assembly of G. rufa using PacBio HiFi long-read sequencing and Hi-C technology. The genome is 1.38 Gb in size, with 25 chromosomes and a scaffold N50 of 49.3 Mb. Approximately 59% of the genome consists of repetitive elements, while 27,352 protein-coding genes were annotated, with 98.3% being functionally characterized. BUSCO analysis revealed 94.5% and 94.7% completeness for the genome assembly and annotated protein sequences, respectively. Notably, we identified two heat shock transcription factor (HSF) genes, 239 heat shock protein (HSP)-related genes, and 1,036 heat shock elements (HSEs) in regulatory regions. Phylogenetic analysis supports the placement of G. rufa within the Labeoninae subfamily. This genome assembly provides a valuable resource for advancing G. rufa as a model organism.
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Affiliation(s)
- Tetsuo Kon
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, 1030, Austria.
| | - Koto Kon-Nanjo
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, 1030, Austria
| | - Kiki Syaputri Handayani
- Research Center for Marine and Land Bioindustry, Research Organization for Earth Sciences and Maritime, BRIN. Jl. Raya Senggigi, Teluk Kodek, 83352, Indonesia
| | - Liqing Zang
- Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie, 514-8507, Japan
- Mie University Zebrafish Research Center, 2-174 Edobashi, Tsu, Mie, 514-8572, Japan
| | - Fahrurrozi Fahrurrozi
- Research Center for Marine and Land Bioindustry, Research Organization for Earth Sciences and Maritime, BRIN. Jl. Raya Senggigi, Teluk Kodek, 83352, Indonesia
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, 1030, Austria
| | - Victor David Nico Gultom
- Research Center for Marine and Land Bioindustry, Research Organization for Earth Sciences and Maritime, BRIN. Jl. Raya Senggigi, Teluk Kodek, 83352, Indonesia
| | - Yasuhito Shimada
- Mie University Zebrafish Research Center, 2-174 Edobashi, Tsu, Mie, 514-8572, Japan.
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, 2-174 Edobashi, Tsu, Mie, 514-8572, Japan.
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26
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Petroll R, West JA, Ogden M, McGinley O, Craig RJ, Coelho SM, Borg M. The expanded Bostrychia moritziana genome unveils evolution in the most diverse and complex order of red algae. Curr Biol 2025:S0960-9822(25)00508-1. [PMID: 40345196 DOI: 10.1016/j.cub.2025.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 04/13/2025] [Accepted: 04/17/2025] [Indexed: 05/11/2025]
Abstract
Red algae are an ancient eukaryotic lineage that were among the first to evolve multicellularity. Although they share a common origin with modern-day plants and display complex multicellular development, comprehensive genome data from the most highly evolved red algal groups remain scarce. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a complex red seaweed in the Rhodomelaceae family of the Ceramiales-the largest and most diverse order of red algae. Contrary to the view that red algal genomes are typically small, we report significant genome size expansion in Bostrychia and other Ceramiales, which represents one of at least three independent expansion events in red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole-genome duplications, but in Bostrychia rather stem from the proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with its enlarged genome, Bostrychia has an increased gene content shaped by de novo gene emergence and amplified gene families in common with other Ceramiales, providing insight into the genetic adaptations underpinning this successful and species-rich order. Finally, our sex-specific assemblies resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, each sex chromosome harbors a three amino acid loop extension homeodomain (TALE-HD) transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this red seaweed lineage can provide insight into the evolutionary origins and universal principles underpinning complex multicellularity.
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Affiliation(s)
- Romy Petroll
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - John A West
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael Ogden
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C 1871, Denmark
| | - Owen McGinley
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Rory J Craig
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen 72076, Germany.
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27
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Kim IV, Navarrete C, Grau-Bové X, Iglesias M, Elek A, Zolotarov G, Bykov NS, Montgomery SA, Ksiezopolska E, Cañas-Armenteros D, Soto-Angel JJ, Leys SP, Burkhardt P, Suga H, de Mendoza A, Marti-Renom MA, Sebé-Pedrós A. Chromatin loops are an ancestral hallmark of the animal regulatory genome. Nature 2025:10.1038/s41586-025-08960-w. [PMID: 40335694 DOI: 10.1038/s41586-025-08960-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/31/2025] [Indexed: 05/09/2025]
Abstract
In bilaterian animals, gene regulation is shaped by a combination of linear and spatial regulatory information. Regulatory elements along the genome are integrated into gene regulatory landscapes through chromatin compartmentalization1,2, insulation of neighbouring genomic regions3,4 and chromatin looping that brings together distal cis-regulatory sequences5. However, the evolution of these regulatory features is unknown because the three-dimensional genome architecture of most animal lineages remains unexplored6,7. To trace the evolutionary origins of animal genome regulation, here we characterized the physical organization of the genome in non-bilaterian animals (sponges, ctenophores, placozoans and cnidarians)8,9 and their closest unicellular relatives (ichthyosporeans, filastereans and choanoflagellates)10 by combining high-resolution chromosome conformation capture11,12 with epigenomic marks and gene expression data. Our comparative analysis showed that chromatin looping is a conserved feature of genome architecture in ctenophores, placozoans and cnidarians. These sequence-determined distal contacts involve both promoter-enhancer and promoter-promoter interactions. By contrast, chromatin loops are absent in the unicellular relatives of animals. Our findings indicate that spatial genome regulation emerged early in animal evolution. This evolutionary innovation introduced regulatory complexity, ultimately facilitating the diversification of animal developmental programmes and cell type repertoires.
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Affiliation(s)
- Iana V Kim
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centre Nacional d'Anàlisis Genòmic (CNAG), Barcelona, Spain.
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marta Iglesias
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Anamaria Elek
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Grygoriy Zolotarov
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Sean A Montgomery
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ewa Ksiezopolska
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Didac Cañas-Armenteros
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Hiroshi Suga
- Department of Life and Environmental Sciences, Faculty of Bioresource Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Alex de Mendoza
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centre Nacional d'Anàlisis Genòmic (CNAG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Barcelona, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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28
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Cheng HY, Jiang LP, Fei Y, Lu F, Ma S. An annotated near-complete sequence assembly of the Magnaporthe oryzae 70-15 reference genome. Sci Data 2025; 12:758. [PMID: 40335505 PMCID: PMC12059122 DOI: 10.1038/s41597-025-05116-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2025] [Accepted: 04/28/2025] [Indexed: 05/09/2025] Open
Abstract
Magnaporthe oryzae is a devastating fungal pathogen that causes substantial yield losses in rice and other cereal crops worldwide. A high-quality genome assembly is critical for addressing challenges posed by this pathogen. However, the current widely used MG8 assembly of the M. oryzae strain 70-15 reference genome contains numerous gaps and unresolved repetitive regions. Here, we report a complete 44.82 Mb high-quality nuclear genome and a 35.95 kb circular mitochondrial genome for strain 70-15, generated using deep-coverage PacBio high-fidelity sequencing (HiFi) and high-resolution chromatin conformation capture (Hi-C) data. Notably, we successfully resolved one or both telomere sequences for all seven chromosomes and achieved telomere-to-telomere (T2T) assemblies for chromosomes 2, 3, 4, 6, and 7. Based on this T2T assembly, we predicted 12,100 protein-coding genes and 493 effectors. This high-quality T2T assembly represents a significant advancement in M. oryzae genomics and provides an enhanced reference for studies in genome biology, comparative genomics, and population genetics of this economically important plant pathogen.
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Affiliation(s)
- Hang-Yuan Cheng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Li-Ping Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yue Fei
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Fei Lu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.
| | - Shengwei Ma
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, P. R. China.
- Yazhouwan National Laboratory, Sanya, Hainan, 572024, P. R. China.
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29
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Xiong M, Cheng R, He B, Wu CS, Zhu CD, Luo A, Zhou QS. Chromosome-level genome assembly of Parotis chlorochroalis (Lepidoptera: Crambidae: Spilomelinae). Sci Data 2025; 12:743. [PMID: 40328770 PMCID: PMC12056075 DOI: 10.1038/s41597-025-05053-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 04/23/2025] [Indexed: 05/08/2025] Open
Abstract
Parotis Hübner, 1831 is a genus within the family Crambidae, which is recognized as one of the most diverse families of Lepidoptera. Species within the genus Parotis can be readily distinguished from other closely related genera by their distinctive green or yellow-green body coloration. However, the genus Parotis has received relatively limited research attention, and the scarcity of genome-wide molecular resources has impeded a more comprehensive understanding of its evolution, adaptation, and phylogenetic relationships. This study reports the first genome assembly for Parotis chlorochroalis (Hampson, 1912), generated through PacBio Hi-Fi and Hi-C sequencing technologies. The assembled genome has a size of 456.23 Mb, comprising 31 chromosomes. Approximately 181.82 Mb, which constitutes 39.85% of the genome, has been identified as repetitive sequences. The genome assembly includes 16,299 protein-coding genes, of which 94.82% have been functionally annotated. This chromosome-level genome assembly not only advance understanding of P. chlorochroalis but also has the potential to facilitate genomic studies of other lepidopteran species.
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Affiliation(s)
- Mei Xiong
- State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Cheng
- State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bo He
- School of Life Sciences, Jinggangshan University, Ji'an, Jiangxi, 343009, China
| | - Chun-Sheng Wu
- State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao-Dong Zhu
- State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Arong Luo
- State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qing-Song Zhou
- State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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30
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Chen L, Wang H, Xu T, Liu R, Zhu J, Li H, Zhang H, Tang L, Jing D, Yang X, Guo Q, Wang P, Wang L, Liu J, Duan S, Liu Z, Huang M, Li X, Lu Z. A telomere-to-telomere gap-free assembly integrating multi-omics uncovers the genetic mechanism of fruit quality and important agronomic trait associations in pomegranate. PLANT BIOTECHNOLOGY JOURNAL 2025. [PMID: 40318230 DOI: 10.1111/pbi.70107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 03/26/2025] [Accepted: 04/09/2025] [Indexed: 05/07/2025]
Abstract
Pomegranate is an important perennial fruit tree distributed worldwide. Reference genomes with gaps and limit gene identification controlling important agronomic traits hinder its functional genomics and genetic improvements. Here, we reported a telomere-to-telomere (T2T) gap-free genome assembly of the distinctive cultivar 'Moshiliu'. The Moshiliu reference genome was assembled into eight chromosomes without gaps, totalling ~366.71 Mb, with 32 158 predicted protein-coding genes. All 16 telomeres and eight centromeres were characterized; combined with FISH analysis, we revealed the atypical telomere units in pomegranate as TTTTAGGG. Furthermore, a total of 16 loci associated with 15 important agronomic traits were identified based on GWAS of 146 accessions. Gene editing and biochemical experiments demonstrated that a 37.2-Kb unique chromosome translocation disrupting the coding domain sequence of PgANS was responsible for anthocyanin-less, knockout of PgANS in pomegranate exhibited a defect in anthocyanin production; a unique repeat expansion in the promoter of PgANR may affected its expression, resulting in black peel; notably, the G → A transversion located at the 166-bp coding domain of PgNST3, which caused a E56K mutation in the PgNST3 protein, closely linked with soft-seed trait. Overexpression of PgNST3A in tomato presented smaller and softer seed coats. The E56K mutation in PgNST3 protein, eliminated the binding ability of PgNST3 to the PgMYB46 promoter, which subsequently affected the thickness of the inner seed coat of soft-seeded pomegranates. Collectively, the validated gap-free genome, the identified genes controlling important traits and the CRISPR-Cas9-mediated gene knockout system all provided invaluable resources for pomegranate precise breeding.
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Affiliation(s)
- Lina Chen
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Hao Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Tingtao Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ruitao Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, China
| | - Juanli Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Haoxian Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- Chuxiong Yunguo Agriculture Technology Research Institute, Chinese Academy of Agricultural Sciences, Chuxiong, Yunnan, China
| | - Huawei Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, China
| | - Liying Tang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Dan Jing
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xuanwen Yang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Peng Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Luwei Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Junhao Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Shuyun Duan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhaoning Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Mengchi Huang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaolong Li
- OMIX Technologies Corporation, Chengdu, China
| | - Zhenhua Lu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Zhongyuan Research Center, Chinese Academy of Agricultural Sciences, Xinxiang, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- Chuxiong Yunguo Agriculture Technology Research Institute, Chinese Academy of Agricultural Sciences, Chuxiong, Yunnan, China
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Athar F, Zheng Z, Riquier S, Zacher M, Lu JY, Zhao Y, Volobaev V, Alcock D, Galazyuk A, Cooper LN, Schountz T, Wang LF, Teeling EC, Seluanov A, Gorbunova V. Limited cell-autonomous anticancer mechanisms in long-lived bats. Nat Commun 2025; 16:4125. [PMID: 40319021 PMCID: PMC12049446 DOI: 10.1038/s41467-025-59403-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/22/2025] [Indexed: 05/07/2025] Open
Abstract
Several bat species live >20-40 years, suggesting that they possess efficient anti-aging and anti-cancer defenses. Here we investigate the requirements for malignant transformation in primary fibroblasts from four bat species Myotis lucifugus, Eptesicus fuscus, Eonycteris spelaea, and Artibeus jamaicensis - spanning the bat evolutionary tree and including the longest-lived genera. We show that bat fibroblasts do not undergo replicative senescence, express active telomerase, and show attenuated SIPs with dampened secretory phenotype. Unexpectedly, unlike other long-lived mammals, bat fibroblasts are readily transformed by two oncogenic "hits": inactivation of p53 or pRb and activation of HRASG12V. Bat fibroblasts exhibit increased TP53 and MDM2 transcripts and elevated p53-dependent apoptosis. M. lucifugus shows a genomic duplication of TP53. We hypothesize that some bat species have evolved enhanced p53 activity as an additional anti-cancer strategy, similar to elephants. Further, the absence of unique cell-autonomous tumor suppressive mechanisms may suggest that in vivo bats may rely on enhanced immunosurveillance.
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Affiliation(s)
- Fathima Athar
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Zhizhong Zheng
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Sebastien Riquier
- School of Biology and Environmental Science, Belfield, University College Dublin, Dublin, Ireland
| | - Max Zacher
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - J Yuyang Lu
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Dominic Alcock
- School of Biology and Environmental Science, Belfield, University College Dublin, Dublin, Ireland
| | - Alex Galazyuk
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Lisa Noelle Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
| | - Emma C Teeling
- School of Biology and Environmental Science, Belfield, University College Dublin, Dublin, Ireland
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA.
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA.
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.
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Wang C, Tan L, Zhang Z, Li X, Xia L, Cao P, Tong H, Ou X, Li S, Zhang J, Li C, Yang J, Jiao WB, Wang S. Haplotype-resolved genome reveals haplotypic variation and the biosynthesis of medicinal ingredients in Areca catechu L. MOLECULAR HORTICULTURE 2025; 5:24. [PMID: 40312749 PMCID: PMC12046898 DOI: 10.1186/s43897-025-00146-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 01/15/2025] [Indexed: 05/03/2025]
Abstract
Areca catechu, as a traditional Chinese medicine, contains a high concentration of therapeutic compounds. However, the biosynthesis of these compounds is largely unexplored. We present a haplotype-resolved genome assembly and annotation for A. catechu, with chromosome-level genome sizes of 2.45 Gb (Ac. Hap1) and 2.49 Gb (Ac. Hap2). A comparative analysis of the haplotypes revealed significant divergence, including multiple Mb-level large inversions. Furthermore, A. catechu shared two whole genome duplications with other palm plants and its genome size had increased due to the insertion of transposons within the last 2.5 million years. By integrating transcriptomics and metabolomics, two tandem genes (AcGNMT1 and AcGNMT2) were negatively associated with guvacine and trigonelline in gene-metabolite interaction network. AcGNMT1, AcGNMT2 and their three homologous genes were involved in the conversion of guvacine to arecoline. Further analyses tested the function of AcUGT71CE15, AcUGT74CJ38, AcUGT87EE5 and AcUGT83S982 as glucosyltransferases, and AcUGT78AP14 was identified as a rhamnosyltransferase involved in flavonol glycosylation. Our study provides a high-quality genome of A. catechu, characterizes the arecoline biosynthetic pathway and expands the understanding of the diversity of UDP-glucosyltransferase and UDP-rhamnosyltransferase, offering insights into the potential of A. catechu for the biosynthesis of bioactive compounds.
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Affiliation(s)
- Chao Wang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Lei Tan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhonghui Zhang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Xianggui Li
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Linghao Xia
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Peng Cao
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Haiyang Tong
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Xumin Ou
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Shixuan Li
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Jianing Zhang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Chun Li
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China
| | - Jun Yang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China.
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China.
| | - Wen-Biao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
| | - Shouchuang Wang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya Hainan, 572025, China.
- National Key Laboratory for Tropical Crop Breeding, College of Tropical Agriculture and Forestry, Hainan University, Sanya Hainan, 572025, China.
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Wang Y, Zhao L, Wang D, Chen K, Luo T, Luo J, Jiang C, He Z, Huang H, Xie J, Jiang Y, Liu J, Ma T. Four near-complete genome assemblies reveal the landscape and evolution of centromeres in Salicaceae. Genome Biol 2025; 26:111. [PMID: 40317068 PMCID: PMC12046899 DOI: 10.1186/s13059-025-03578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Accepted: 04/15/2025] [Indexed: 05/04/2025] Open
Abstract
BACKGROUND Centromeres play a crucial role in maintaining genomic stability during cell division. They are typically composed of large arrays of tandem satellite repeats, which hinder high-quality assembly and complicate our efforts to understand their evolution across species. Here, we use long-read sequencing to generate near-complete genome assemblies for two Populus and two Salix species belonging to the Salicaceae family and characterize the genetic and epigenetic landscapes of their centromeres. RESULTS The results show that only limited satellite repeats are present as centromeric components in these species, while most of them are located outside the centromere but exhibit a homogenized structure similar to that of the Arabidopsis centromeres. Instead, the Salicaceae centromeres are mainly composed of abundant transposable elements, including CRM and ATHILA, while LINE elements are exclusively discovered in the poplar centromeres. Comparative analysis reveals that these centromeric repeats are extensively expanded and interspersed with satellite arrays in a species-specific and chromosome-specific manner, driving rapid turnover of centromeres both in sequence compositions and genomic locations in the Salicaceae. CONCLUSIONS Our results highlight the dynamic evolution of diverse centromeric landscapes among closely related species mediated by satellite homogenization and widespread invasions of transposable elements and shed further light on the role of centromere in genome evolution and species diversification.
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Affiliation(s)
- Yubo Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Lulu Zhao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Kai Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Tiannan Luo
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Jianglin Luo
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Chengzhi Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Zhoujian He
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Heng Huang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Jiaxiao Xie
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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Chen X, Jiang T, Xue J, Gu M, Wang M, Liu K. Chromosome-level genome assembly of the freshwater bivalve Anodonta woodiana. Sci Data 2025; 12:731. [PMID: 40316565 PMCID: PMC12048480 DOI: 10.1038/s41597-025-05078-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Accepted: 04/28/2025] [Indexed: 05/04/2025] Open
Abstract
The freshwater bivalve Anodonta (Sinanodonta) woodiana originated in the Yangtze River basin of China and is now widely distributed in Asia, Europe, North America, and Africa. This species has important economic and ecological value. Using Illumina, PacBio, and Hi-C technology, a high-quality chromosome-level genome of A. woodiana was assembled. The genome size was 2.80 Gb, with a contig N50 of 4.01 Mb and a scaffold N50 of 143.34 Mb. In total, 1609 contigs, accounting for 99.57% of the total assembled genome, were anchored into 19 chromosomes. In total, 1.51 Gb repeat sequences were annotated and 44,785 protein-coding genes were predicted. This study is the first to reveal the genome of A. woodiana and the genus Anodonta, which will effectively contribute to investigations of this species' biology, molecular mechanisms in response to environmental stress, and resource management.
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Affiliation(s)
- Xiubao Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Tao Jiang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Junren Xue
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Mengying Gu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Meiyi Wang
- College of Marine Science and Technology and Environment, Dalian Ocean University, Dalian, 116023, China
| | - Kai Liu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
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Moffett AS, Falcón-Cortés A, Di Pierro M. Quantifying the influence of genetic context on duplicated mammalian genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.03.647042. [PMID: 40236061 PMCID: PMC11996522 DOI: 10.1101/2025.04.03.647042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Gene duplication is a fundamental part of evolutionary innovation. While single-gene duplications frequently exhibit asymmetric evolutionary rates between paralogs, the extent to which this applies to multi-gene duplications remains unclear. In this study, we investigate the role of genetic context in shaping evolutionary divergence within multi-gene duplications, leveraging microsynteny to differentiate source and target copies. Using a dataset of 193 mammalian genome assemblies and a bird outgroup, we systematically analyze patterns of sequence divergence between duplicated genes and reference orthologs. We find that target copies, those relocated to new genomic environments, exhibit elevated evolutionary rates compared to source copies in the ancestral location. This asymmetry is influenced by the distance between copies and the size of the target copy. We also demonstrate that the polarization of rate asymmetry in paralogs, the "choice" of the slowly evolving copy, is biased towards collective, block-wise polarization in multi-gene duplications. Our findings highlight the importance of genetic context in modulating post-duplication divergence, where differences in cis-regulatory elements and co-expressed gene clusters between source and target copies may be responsible. This study presents a large-scale test of asymmetric evolution in multi-gene duplications, offering new insight into how genome architecture shapes functional diversification of paralogs.
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Xu H, Han Y, Chi X, Yu J, Xia M, Han S, Niu Y, Zhang F, Chen S. Integration of De Novo Chromosome-Level Genome and Population Resequencing of Peganum (Nitrariaceae): A Case Study of Speciation and Evolutionary Trajectories in Arid Central Asia. Mol Ecol Resour 2025; 25:e14078. [PMID: 39925320 DOI: 10.1111/1755-0998.14078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 12/19/2024] [Accepted: 01/27/2025] [Indexed: 02/11/2025]
Abstract
Natural hybridization is a significant driving force in plant evolution and speciation. Understanding the genetic mechanism and dynamic evolutionary trajectories of divergence between species and hybrids remains a central goal in evolutionary biology. Here, we examined the genetic divergence of Peganum and their intermittent and hybrid entities (IHEs) from large-scale sympatric and allopatric regions. We sequenced the genomes of Peganum from the Arid Central Asia (ACA) region and its surrounding areas, discovering that the origin of Peganum could be traced to the Hexi Corridor in eastern Central Asia, where migration led to geographic and environmental isolation, giving rise to new species based on natural selection. Different Peganum species, exhibiting excellent dispersal abilities, migrated to the same regions and underwent hybridization. The descendant species of Peganum inherited and developed adaptive traits from parent species through gene flow and introgression, particularly in DNA repair and wax layer formation, leading to the speciation of the IHEs. This study clarified the transition stages in hybrid speciation and identified the Mixing-Isolation-Mixing cycles (MIM) model as a speciation framework suitable for Peganum, marking the initial identification of this unique evolutionary model in the ACA region.
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Affiliation(s)
- Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingze Xia
- School of Pharmacy, Shandong Second Medical University, Weifang, China
| | - Shuang Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Niu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
- Xining Botanical Garden, Xining, China
| | - Shilong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology & Institute of Sanjiangyuan National Park, Chinese Academy of Sciences, Xining, China
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Xining, China
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Yang Y, Chen J, Hu X. Gap-free genome assembly and comparative analysis reveal the evolution and lignin degradation mechanisms of Cylindrobasidium torrendii. Genomics 2025; 117:111029. [PMID: 40068802 DOI: 10.1016/j.ygeno.2025.111029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 02/17/2025] [Accepted: 03/06/2025] [Indexed: 03/20/2025]
Abstract
The Physalacriaceae family comprises numerous saprophytic edible and medicinal fungi with significant ecological and economic importance. However, the lack of high-quality genomic data has hindered systematic studies of this family. Here, we report the chromosome-level genome assembly of Cylindrobasidium torrendii, a species identified in China, using a combination of Illumina, PacBio HiFi, and Hi-C sequencing technologies. The 33.67 Mb genome, featuring a GC content of 52.00 %, demonstrates enhanced continuity and completeness. Phylogenetic analysis based on 1685 single-copy orthologous gene families places C. torrendii in close evolutionary proximity to Armillaria mellea and Gymnopus necrorhizus, with a divergence time of 112.39 Mya. Comparative genomics reveals conserved syntenic blocks between chromosomes of C. torrendii and those of Pleurotus ostreatus and Lentinula edodes. Gene family analysis identified 980 expanded and 487 contracted gene families, with expanded genes significantly enriched in secondary metabolite biosynthesis pathways. CAZyme, P450, and laccase gene family comparisons highlighted the evolutionary dynamics of these gene families in C. torrendii. Transcriptomic analysis under fungal dark stress revealed significant upregulation of genes such as CtoLAC7 and CAZymes (GH and CE families). This study provides a high-quality genomic resource and novel insights into the genetic and functional characteristics of C. torrendii and the Physalacriaceae family.
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Affiliation(s)
- Yang Yang
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Chen
- Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Colorectal Cancer Clinical Research Center of Hubei Province, Colorectal Cancer Clinical Research Center of Wuhan, Wuhan 430070, China.
| | - Xuebo Hu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China.
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Yu H, Wang H, Liang X, Liu J, Jiang C, Chi X, Zhi N, Su P, Zha L, Gui S. Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus. HORTICULTURE RESEARCH 2025; 12:uhaf030. [PMID: 40224331 PMCID: PMC11992332 DOI: 10.1093/hr/uhaf030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 01/29/2025] [Indexed: 04/15/2025]
Abstract
Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory and hepatoprotective properties. P. grandiflorus has important clinical value because of the active triterpenoid saponins in its roots. However, the biosynthetic pathway of triterpenoid saponins in P. grandiflorus remains unclear, and the related genes remain unknown. Therefore, in this study, we assembled a high-quality and integrated telomere-to-telomere P. grandiflorus reference genome and combined time-specific transcriptome and metabolome profiling to identify the cytochrome P450s (CYPs) responsible for the hydroxylation processes involved in triterpenoid saponin biosynthesis. Nine chromosomes were assembled without gaps or mismatches, and nine centromeres and 18 telomere regions were identified. This genome eliminated redundant sequences from previous genome versions and incorporated structural variation information. Comparative analysis of the P. grandiflorus genome revealed that P. grandiflorus underwent a core eudicot γ-WGT event. We screened 211 CYPs and found that tandem and proximal duplications may be crucial for the expansion of CYP families. We outlined the proposed hydroxylation steps, likely catalyzed by the CYP716A/72A/749A families, in platycodin biosynthesis and identified three PgCYP716A, seven PgCYP72A, and seven PgCYP749A genes that showed a positive correlation with platycodin biosynthesis. By establishing a T2T assembly genome, transcriptome, and metabolome resource for P. grandiflorus, we provide a foundation for the complete elucidation of the platycodins biosynthetic pathway, which consequently leads to heterologous bioproduction, and serves as a fundamental genetic resource for molecular-assisted breeding and genetic improvement of P. grandiflorus.
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Affiliation(s)
- Hanwen Yu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Haixia Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Xiao Liang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Juan Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chao Jiang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiulian Chi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Nannan Zhi
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Ping Su
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Liangping Zha
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
- Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei 230012, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei 230012, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Shuangying Gui
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei 230012, China
- Institute of Pharmaceutics, Anhui Academy of Chinese Medicine, Hefei 230012, China
- Anhui Province Key Laboratory of Pharmaceutical Preparation Technology and Application, Hefei 230012, China
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Adaskaveg JA, Lee C, Wei Y, Wang F, Grilo FS, Mesquida‐Pesci SD, Davis M, Wang SC, Marino G, Ferguson L, Brown PJ, Drakakaki G, Morales AM, Marchese A, Giovino A, Burgos EM, Marra FP, Cuevas LM, Cattivelli L, Bagnaresi P, Carbonell‐Bejerano P, Monroe JG, Blanco‐Ulate B. In a nutshell: pistachio genome and kernel development. THE NEW PHYTOLOGIST 2025; 246:1032-1048. [PMID: 40107319 PMCID: PMC11982797 DOI: 10.1111/nph.70060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 02/19/2025] [Indexed: 03/22/2025]
Abstract
Pistachio is a sustainable nut crop with exceptional climate resilience and nutritional value. However, the molecular processes underlying pistachio nut development and nutritional traits are largely unknown, compounded by limited genomic and molecular resources. To advance pistachios as a future food source and a model system for hard-shelled fruits, we generated a chromosome-scale reference genome of the most widely grown pistachio cultivar (Pistacia vera 'Kerman') and a spatiotemporal study of nut development. We integrated tissue-level physiological data from thousands of nuts over three growing seasons with transcriptomic data encompassing 14 developmental time points of the hull, shell, and kernel to assemble gene modules associated with physiological changes. Our study defined four distinct stages of pistachio nut growth and maturation. We then focused on the kernel to identify transcriptional and metabolic changes in molecular pathways governing nutritional quality, such as the accumulation of unsaturated fatty acids, which are vital for shelf life and dietary value. These findings revealed key candidate conserved regulatory genes, such as PvAP2-WRI1 and PvNFYB-LEC1, likely involved in oil accumulation in kernels. This work yields new knowledge and resources that will inform other woody crops and facilitate further improvement of pistachio as a globally significant, sustainable, and nutritious crop.
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Affiliation(s)
| | - Chaehee Lee
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Yiduo Wei
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Fangyi Wang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Filipa S. Grilo
- Corto OliveLodiCA95212USA
- Department of Food Science and TechnologyUniversity of California DavisDavisCA95616USA
| | | | - Matthew Davis
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Selina C. Wang
- Department of Food Science and TechnologyUniversity of California DavisDavisCA95616USA
| | - Giulia Marino
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Louise Ferguson
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Patrick J. Brown
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | | | - Adela Mena Morales
- Regional Institute of Agri‐Food and Forestry Research and Development of Castilla‐La Mancha (IRIAF), IVICAM, CTRAToledo‐Albacete s/n, 13700Tomelloso (Ciudad Real)13700Spain
| | - Annalisa Marchese
- Department of Agricultural, Food and Forest SciencesUniversity of PalermoViale delle Scienze – Ed. 4Palermo90128Italy
| | - Antonio Giovino
- CREA for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA‐DC)Viale delle ScienzePalermo90128Italy
| | - Esaú Martínez Burgos
- Regional Institute of Agri‐Food and Forestry Research and Development of Castilla‐La Mancha (IRIAF), IVICAM, CTRAToledo‐Albacete s/n, 13700Tomelloso (Ciudad Real)13700Spain
| | - Francesco Paolo Marra
- Department of Agricultural, Food and Forest SciencesUniversity of PalermoViale delle Scienze – Ed. 4Palermo90128Italy
| | - Lourdes Marchante Cuevas
- Regional Institute of Agri‐Food and Forestry Research and Development of Castilla‐La Mancha (IRIAF), IVICAM, CTRAToledo‐Albacete s/n, 13700Tomelloso (Ciudad Real)13700Spain
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and BioinformaticsFiorenzuola d'Arda29017Italy
| | - Paolo Bagnaresi
- CREA Research Centre for Genomics and BioinformaticsFiorenzuola d'Arda29017Italy
| | - Pablo Carbonell‐Bejerano
- Instituto de Ciencias de la Vid y del Vino, ICVV, for Grape and Wine Sciences ICVV, CSIC – Universidad de La Rioja – Gobierno de La RiojaLogroño26007Spain
| | - J. Grey Monroe
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
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Zhou T, Huang XJ, Cheng YJ, Zhang XY, Wang XJ, Li ZH. Telomere-to-telomere genome and multi-omics analysis of Prunus avium cv. Tieton provides insights into its genomic evolution and flavonoid biosynthesis. Int J Biol Macromol 2025; 306:141809. [PMID: 40057088 DOI: 10.1016/j.ijbiomac.2025.141809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 02/17/2025] [Accepted: 03/05/2025] [Indexed: 05/11/2025]
Abstract
The European sweet cherry (Prunus avium) is highly valued for its superior quality, delectable taste, and robust stress resistance, leading to its extensive cultivation in the world. However, the previous incomplete genome assemblies have impeded its evolution and genetic regulation studies. In this study, we generated a Telomere-to-Telomere gap-free genome assembly of P. avium cv. Tieton, using advanced sequencing technologies. The assembled genome comprises eight pseudochromosomes with a genome size of 342.23 Mb and a contig N50 of 40.66 Mb. Comparative genomic analysis identified several unique stress resistance-related genes, possibly associated with the species' environmental adaptation. The integrative analyses of genomics, transcriptomes and metabolomes identified some key structural genes and metabolites crucial to flavonoid biosynthesis of sweet cherry. Our analyses revealed that 85 flavonoid metabolites, which are highly differentially accumulated among five tissues (flesh, stem, leaf, bud, and seed) of cherry. Interestingly, eight abundant flavonoids (Narcissoside, Typhaneoside, Myricetin 3-0-galactoside, Diosmin, Neohesperidin, Liquiritin apioside, 5,6,7-Trimethoxyflavone and Oroxin B) were highly accumulated in cherry flesh tissues. The gene-metabolite correlation analysis revealed that seven genes (HTC8, HTC6, CYP75B1_9, CYP75B1_10, 4CL1, DFR1, and FLS1) significantly regulated flavonoid accumulation in cherry flesh. Additionally, some structural genes (4CL6, PAL3, CYP75A2, F3H1, CYP75B1_8, and CYP75B1_10) were identified in the flavonoid biosynthetic pathway and were highly expressed, aligning with high flavonoid metabolite content in cherry flesh. These identified genes and metabolites are likely pivotal in conferring sweet cherry's stress resistance and high-quality traits. These findings offer deep insights into the mechanisms of genomic evolution and flavonoid biosynthesis, which also lay a solid foundation for further function genomics studies and breeding improvement in cherry.
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Affiliation(s)
- Tong Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Xiao-Juan Huang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yan-Jun Cheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Xing-Ya Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Xiao-Juan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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Cox K, Gouwy J, Mergeay J, Neyrinck S, Van Den Berge K. Rapid Colonisation of Synanthropic Stone Martens in a Highly Urbanised Region: Insights From Temporal and Spatial Analysis. Ecol Evol 2025; 15:e71392. [PMID: 40421061 PMCID: PMC12104667 DOI: 10.1002/ece3.71392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 04/15/2025] [Accepted: 04/20/2025] [Indexed: 05/28/2025] Open
Abstract
Medium-sized carnivores, including the synanthropic stone marten (Martes foina Erxleben, 1777), have shown remarkable adaptability to urbanised and fragmented landscapes, facilitating their spread across mainland Europe. This study investigates the recolonisation of a highly urbanised region by stone martens within two decades, examining spatial and temporal genome-wide data (using genotyping by sequencing) to reveal colonisation dynamics, sources, and barriers influencing their expansion. Using genotypes from 5536 SNPs across 376 stone martens collected between 1995 and 2013, our findings indicate that stone martens successfully expanded through urban environments, yet dispersal was neither entirely random nor strictly distance-dependent. The initial southeastern stronghold (E1) showed the lowest genetic diversity and limited spatial expansion, while other population sources contributed to recolonisation, highlighting a complex, multi-source expansion. Gene flow in the early stages was largely confined to E1, progressing northward and eventually enabling exchange with a second eastern lineage (E2). Meanwhile, the western lineage displayed higher connectivity, occasionally crossing barriers like motorways. Motorways, however, significantly shaped recolonisation patterns, reducing gene flow, while other elements such as built-up areas, secondary roads or waterways showed an additional though very small effect. Over the study period, genetic patch size increased, indicating longer dispersal distances. Gene flow strengthened within both eastern (E1 and E2) and western populations. Still, the western population diverged into two subclusters (W1 and W2) of which one became more differentiated. This suggests limited genetic homogenisation in the near future. This study provides insights into the genetic and ecological dynamics of carnivore recolonisation in highly fragmented landscapes.
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Affiliation(s)
- Karen Cox
- Research Institute for Nature and Forest (INBO)GeraardsbergenBelgium
| | - Jan Gouwy
- Research Institute for Nature and Forest (INBO)GeraardsbergenBelgium
| | - Joachim Mergeay
- Research Institute for Nature and Forest (INBO)GeraardsbergenBelgium
| | - Sabrina Neyrinck
- Research Institute for Nature and Forest (INBO)GeraardsbergenBelgium
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Liu C, Li D, Dang J, Shu J, Smit SJ, Wu Q, Lichman BR. Haplotype-resolved genome of Agastache rugosa (Huo Xiang) provides insight into monoterpenoid biosynthesis and gene cluster evolution. HORTICULTURE RESEARCH 2025; 12:uhaf034. [PMID: 40224328 PMCID: PMC11992331 DOI: 10.1093/hr/uhaf034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 01/25/2025] [Indexed: 04/15/2025]
Abstract
Monoterpenoids are small volatile molecules produced by many plants that have applications in consumer products and healthcare. Plants from the mint family (Lamiaceae) are prodigious producers of monoterpenoids, including a chemotype of Agastache rugosa (Huo Xiang), which produces pulegone and isomenthone. We sequenced, assembled and annotated a haplotype-resolved chromosome-scale genome assembly of A. rugosa with a monoterpene chemotype. This genome assembly revealed that pulegone biosynthesis genes are in a biosynthetic gene cluster, which shares a common origin with the pulegone gene cluster in Schizonepeta tenuifolia. Using phylogenetics and synteny analysis, we describe how the clusters in these two species diverged through inversions and duplications. Using Hi-C analysis, we identified tentative evidence of contact between the pulegone gene cluster and an array of pulegone reductases, with both regions also enriched in retrotransposons. This genome and its analysis add valuable and novel insights to the organization and evolution of terpenoid biosynthesis in Lamiaceae.
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Affiliation(s)
- Chanchan Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - DiShuai Li
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jingjie Dang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Juan Shu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Samuel J Smit
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD, UK
| | - QiNan Wu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Benjamin R Lichman
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD, UK
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Wang Y, Huang D, Luo J, Yao S, Chen J, Li L, Geng J, Mo Y, Ming R, Liu J. The chromosome-level genome of Centella asiatica provides insights into triterpenoid biosynthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 222:109710. [PMID: 40054110 DOI: 10.1016/j.plaphy.2025.109710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 02/19/2025] [Accepted: 02/24/2025] [Indexed: 05/07/2025]
Abstract
Centella asiatica is a well-known herbal plant that makes a significant contribution to the treatment of various chronic ailments. Triterpenoid saponins are the main active components extracted from C. asiatica, which have rich pharmacological activity. However, only a few studies have systematically elucidated the molecular mechanism underlying the biosynthesis of triterpenoid saponins in C. asiatica. Here, we report a chromosome-level reference genome of C. asiatica, by using Illumina, PacBio HiFi, and Hi-C technologies. The assembled genome exhibits high quality with a size of 455 Mb and a contig N50 of 36 Mb. A total of 26,479 protein-coding genes were predicted. Comparative genomic analysis revealed that the gene families involved in triterpenoid saponin biosynthesis, including squalene synthase (SS) and farnesyl diphosphate synthase (FPS), rapidly expanded in the C. asiatica genome. In particular, we have discovered two whole-genome duplication events in C. asiatica genomes. A further comprehensive analysis of the metabolome and transcriptome was performed using different tissues of C. asiatica in order to identify the key genes associated with triterpenoid saponin biosynthesis. Consequently, seven enzyme genes were considered to play important roles in triterpenoid biosynthesis. Subsequent functional characterization of CaOSC4 demonstrated that it is responsible for the biosynthesis of three ursane-type triterpenoids in C. asiatica. Our research establishes a genomic data platform that can be employed in the excavation of genes and precision breeding in C. asiatica. Additionally, the results offer new insights into the biosynthesis of triterpenoid saponins.
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Affiliation(s)
- Yue Wang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China; National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ding Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Jiajia Luo
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Shaochang Yao
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Jianhua Chen
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Liangbo Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Jingjing Geng
- National Engineering Research Center for Agriculture in Northern Mountainous Areas/College of Horticulture, Hebei Agricultural University, Baoding, 071000, China
| | - Yanlan Mo
- Guilin Yiyuansheng, Modern Biotechnology Co., Ltd, Guilin, 541004, China
| | - Ruhong Ming
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning, 530200, China.
| | - Jihong Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.
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44
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Zhu Z, Yang X, Kang W, Cai C, Zhou Q. Chromosome-Level Genome Assembly and Annotation of the Amur Rat Snake Elaphe schrenckii. Genome Biol Evol 2025; 17:evaf086. [PMID: 40333365 PMCID: PMC12089936 DOI: 10.1093/gbe/evaf086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 04/26/2025] [Accepted: 04/29/2025] [Indexed: 05/09/2025] Open
Abstract
The Amur rat snake (Elaphe schrenckii), a widely distributed colubrid species in Northeast Asia, plays a critical role in controlling rodent and mouse populations in the wild. Despite its ecological and evolutionary significance, genomic resources for this nonvenomous species have been limited. In this study, we present a high-quality, chromosome-level genome assembly of E. schrenckii, generated by PacBio HiFi long-read sequencing and Hi-C chromatin interaction mapping. The assembled genome size comprises 1.69 Gb, with a scaffold N50 length of 215 Mb. Hi-C scaffolding anchored the genome into 18 chromosomes, including one that represents the conserved Z chromosome of snakes, consistent with karyotypic observations. This assembly enables further gene annotation and analysis of chromosomal synteny patterns. Repetitive elements account for 53.2% of the genome, with long interspersed nuclear element retrotransposons being the predominant class (23.2%). We identified 18,529 protein-coding genes, with 90.6% functionally annotated through homology-based methods. The genome assembly is highly complete, with a BUSCO score of 97.4% (tetrapoda_odb10). This resource provides a foundation for comparative studies of colubrid genome evolution, which also serves as a crucial reference for conservation genomics, particularly for Asian snake populations facing habitat fragmentation.
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Affiliation(s)
- Zexian Zhu
- Center for Evolutionary and Organismal Biology and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xusheng Yang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wen Kang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Cheng Cai
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qi Zhou
- Center for Evolutionary and Organismal Biology and Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Center for Reproductive Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- State Key Laboratory of Transvascular Implantation Devices, Zhejiang University, Hangzhou, China
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45
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Zhang R, Wnag M, Zhang G, Gao X, Xiang N, Liu S, Zhao Y, Qin L, Yuan T. Chromosomal level genome assembly of medicinal plant Rosa laevigata. Sci Data 2025; 12:716. [PMID: 40307259 PMCID: PMC12043960 DOI: 10.1038/s41597-025-05025-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 04/16/2025] [Indexed: 05/02/2025] Open
Abstract
Rosa laevigata Michx., an endemic perennial herbaceous plant in China, possesses significant medicinal value in traditional herbal practices. However, the absence of a reference genome has hindered its development and utilization. In this study, we present a chromosome-level de novo genome assembly of two haplotypes (Hap1 and Hap2) of R. laevigata by integration of Hifi long reads, BGI short reads, and Hi-C reads. The assembled Hap1 genome spans 493 Mb, Hap2 genome spans 479 Mb, and both of them were assigned to 7 chromosomes each. The mapping rate of BGI short reads to the two haplotypes genome is approximately 99.26% and 99.23%, and BUSCO assessment reveals that 98.6% and 98.7% of the genes are complete. Furthermore, we predicted 43,480 and 41,251 protein-coding genes in two haplotype genomes, respectively. The chromosome-level genome of R. laevigata enhances the genetic resources available for Rosa species and lays the groundwork for subsequent medicinal development.
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Affiliation(s)
- Rongxiang Zhang
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China
| | - Maohui Wnag
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Guiyu Zhang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaoman Gao
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Niyan Xiang
- School of Resources and Environmental Science, Hubei University, Wuhan, 430062, China
| | - Shuwen Liu
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China
| | - Yuemei Zhao
- School of Biological Science, Guizhou Education University, Guiyang, 550018, China
| | - Lijun Qin
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Tao Yuan
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- School of Ecology and Environment, Tibet University, Tibet, China.
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46
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Liang YY, Liu H, Lin QQ, Shi Y, Zhou BF, Wang JS, Chen XY, Shen Z, Qiao LJ, Niu JW, Ling SJ, Luo WJ, Zhao W, Liu JF, Kuang YW, Ingvarsson PK, Guo YL, Wang B. Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species. Mol Biol Evol 2025; 42:msaf088. [PMID: 40235155 PMCID: PMC12042805 DOI: 10.1093/molbev/msaf088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 04/01/2025] [Accepted: 04/02/2025] [Indexed: 04/17/2025] Open
Abstract
The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.
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Affiliation(s)
- Yi-Ye Liang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Hui Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
| | - Qiong-Qiong Lin
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Yong Shi
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Biao-Feng Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Jing-Shu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Xue-Yan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Zhao Shen
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Liang-Jing Qiao
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Jing-Wei Niu
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Shao-Jun Ling
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Wen-Ji Luo
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
| | - Jian-Feng Liu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuan-Wen Kuang
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Baosheng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
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Li P, Fan X, Li S, Tong Y, Tian Z, Zhang Y, Wu S, Wang C, Xiao Y, Wang G, Bai M. Chromosome-level genome assembly of the sap beetle Glischrochilus (Librodor) japonius (Coleoptera: Nitidulidae). Sci Data 2025; 12:711. [PMID: 40301379 PMCID: PMC12041576 DOI: 10.1038/s41597-025-04774-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 03/06/2025] [Indexed: 05/01/2025] Open
Abstract
Sap beetles are widely distributed in the Holarctic and tropical regions, with diverse feeding habits and strong adaptability. They play important roles in the decay of plants, the spread of fungi and bacteria, and the carbon and nitrogen cycles in agricultural ecosystems. Here, we provide an annotated, chromosome level reference genome assembly for a sap beetle Glischrochilus (Librodor) japonius (Motschulsky, 1857), a member of the family Nitidulidae, assembled using PacBio HiFi and Hi-C data from female specimens. The final assembly has a total size of 789.06 Mb, with 94.91% of the sequence successfully anchored to 10 chromosomes. The scaffold N50 is 77.84 Mb, and BUSCO (endopterygota_odb10 database) completeness is 97.20%. Repetitive elements comprise 54.67% of the genome (431.38 Mb). We identified 1,673 noncoding RNAs and predicted 22,526 protein-coding genes in the genome. This genome will serve as a valuable resource for advancing our understanding of the evolution and ecology of sap beetles, and will facilitate comparative studies of genome structure within the Nitidulidae family.
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Affiliation(s)
- Panpan Li
- Guangxi Key Laboratory of Agro-environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinyuan Fan
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, Guangxi, 541001, China
| | - Sheng Li
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yijie Tong
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhehao Tian
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Forestry and Prataculture, Ningxia University, Yinchuan, Ningxia, 750021, China
| | - Yingming Zhang
- Guangdong Chebaling National Nature Reserve, Shaoguan, Guangdong, 512500, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, Hunan, China.
| | - Can Wang
- Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Changsha, Hunan, China
| | - Guoquan Wang
- Guangxi Key Laboratory of Agro-environment and Agric-products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, Guangxi, 530004, China.
| | - Ming Bai
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin, 150040, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
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48
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Hu Y, Wang J, Liu L, Yi X, Wang X, Wang J, Hao Y, Qin L, Li K, Feng Y, Zhang Z, Wu H, Jiao Y. Evolutionary history of magnoliid genomes and benzylisoquinoline alkaloid biosynthesis. Nat Commun 2025; 16:4039. [PMID: 40301376 PMCID: PMC12041406 DOI: 10.1038/s41467-025-59343-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Accepted: 04/20/2025] [Indexed: 05/01/2025] Open
Abstract
Benzylisoquinoline alkaloids (BIAs) are important metabolites synthesized in early-diverging eudicots and magnoliids, yet the genetic basis of BIA biosynthesis in magnoliids remains unclear. Here, we decode the genomes of two magnoliid species, Saruma henryi and Aristolochia manshuriensis, and reconstruct the ancestral magnoliid karyotype and infer the chromosomal rearrangement history following magnoliid diversification. Metabolomic, transcriptomic, and phylogenetic analyses reveal the intermediate chemical components and genetic basis of BIA biosynthesis in A. manshuriensis. Although the core enzymes involved in BIA synthesis appear to be largely conserved between early-diverging eudicots and magnoliids, the biosynthetic pathways in magnoliids seem to exhibit greater flexibility. Significantly, our investigation of the evolutionary history of BIA biosynthetic genes revealed that almost all were duplicated before the emergence of extant angiosperms, with only early-diverging eudicots and magnoliids preferentially retaining these duplicated genes, thereby enabling the biosynthesis of BIAs in these groups.
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Affiliation(s)
- Yiheng Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Lumei Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yi
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianyu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya'nan Hao
- Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Liuyu Qin
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Zhongshuai Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Hanying Wu
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
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Zeng Y, Cai Y, Zhou X, Wang S, Li L, Yao Y, Yu J, Liu X, Yang H, Wei T, Dong S, Liu Y. Chromosome-level genomes of Arctic and Antarctic mosses: Aulacomnium turgidum and Polytrichastrum alpinum. Sci Data 2025; 12:705. [PMID: 40301385 PMCID: PMC12041281 DOI: 10.1038/s41597-025-04960-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 04/07/2025] [Indexed: 05/01/2025] Open
Abstract
Bryophytes play a crucial role in the ecosystems of polar regions. These simple plants are among the predominant vegetation types in both Arctic and Antarctic landscapes, where they contribute significantly to biodiversity and ecological stability. Here, we report the chromosome-level genomes of two polar moss species, the Arctic Aulacomnium turgidum and Antarctic Polytrichastrum alpinum. Utilizing a combination of Illumina short reads, Nanopore long reads, and Hi-C data, we assembled genomes of 277.84 Mb for A. turgidum and 498.33 Mb for P. alpinum, respectively. These assemblies were anchored to 11 chromosomes for A. turgidum and 8 chromosomes for P. alpinum. Both species exhibited a sex chromosome with distinct genomic characteristics. Gene annotations revealed 25,999 protein-coding genes in A. turgidum and 28,070 in P. alpinum. The high completeness of the gene space was validated via BUSCO, achieving impressive scores of 98.2% and 98.0%. These high-quality genomes provide critical resources for studying the adaptive evolution and stress tolerance mechanisms of mosses in extreme polar environments.
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Affiliation(s)
- Yuying Zeng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Yuqing Cai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Xuping Zhou
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Sibo Wang
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Linzhou Li
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Yifeng Yao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jin Yu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Xin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Huanming Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Tong Wei
- BGI Research, Wuhan, 430074, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yang Liu
- BGI Research, Wuhan, 430074, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China.
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50
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Xiu C, Zhao D, Zhang J, Liu H, Wang Y, Liu H, Cai X, Luo Z, Bian L, Fu N, Zhou L, Chen Z, Li Z. Chromosome-level genome assembly of Dendrothrips minowai and genomic analysis highlights distinct adaptations to high polyphenols in tea plants. PEST MANAGEMENT SCIENCE 2025. [PMID: 40271779 DOI: 10.1002/ps.8781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 03/04/2025] [Accepted: 03/07/2025] [Indexed: 04/25/2025]
Abstract
BACKGROUND Dendrothrips minowai Priesner, a significant pest in tea-producing regions of Asia, particularly China, damages tea plants (Camellia sinensis) by feeding on their tender leaves rich in polyphenols. Seven assembled genomes from the order Thysanoptera are currently available. RESULTS This study presents the first chromosome-level genome assembly of D. minowai generated by PacBio Revio, Oxford Nanopore Technologies, MGI, and Hi-C technology. The assembled genome measures 350.11 Mb with 1269 contigs with a contig N50 of 536.34 Kb and a scaffold N50 of 16.86 Mb, organized across 19 chromosomes. A total of 16 730 protein-coding genes were identified, with 92.28% functionally annotated. The phylogenetic analysis reveals that D. minowai diverged approximately 103.2 million years ago, preceding all reported genomes of Thripidae species. Comparative genomic analysis identified 12 expanded and 172 contracted gene families of D. minowai, with expanded gene families linked to host plant metabolite processing and detoxification enzymes. Additionally, oligophagous thrips, D. minowai and Stenchaetothrips biformis, possess fewer chemosensory genes (gustatory receptors, odorant receptors, ionotropic receptors, chemosensory proteins, and odorant binding proteins) and detoxification genes (P450s, carboxyl/cholinesterases, UDP-glycosyltransferases) than polyphagous species (Frankliniella occidentalis and Thrips palmi). Interestingly, D. minowai exhibits an expansion in ABC transporter families, especially ABCG and ABCC, which is likely essential for detoxifying the high polyphenol content in tea plants. CONCLUSION This study provides another genome sequence for oligophagous thrips species, which enriches the genomic data for further studies on the evolution, host adaptation, and novel control strategies of thrips. © 2025 Society of Chemical Industry.
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Affiliation(s)
- Chunli Xiu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Dehai Zhao
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- School of Tea Science, Anhui Agricultural University, Hefei, China
| | - Jiahui Zhang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Haitao Liu
- Weifang Natural Resources and Planning Bureau, Weifang, China
| | - Yusheng Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Hangwei Liu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiaoming Cai
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zongxiu Luo
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Lei Bian
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Nanxia Fu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Li Zhou
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zongmao Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Zhaoqun Li
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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