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Chen H, Zhong S, Liu Z, Hu Z, Wang C, Zhou Y, Xu N, Zhao F, Li D, Hu Y. Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation. Food Chem 2025; 481:143980. [PMID: 40154057 DOI: 10.1016/j.foodchem.2025.143980] [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: 01/04/2025] [Revised: 03/04/2025] [Accepted: 03/19/2025] [Indexed: 04/01/2025]
Abstract
Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.
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Affiliation(s)
- Haiyin Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China
| | - Sicheng Zhong
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China
| | - Zhijie Liu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China
| | - Zhao Hu
- Hubei Lulingwang Liquor Industry Co., Ltd, Fangxian 442399, Hubei, China
| | - Chao Wang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China
| | - Yuke Zhou
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China
| | - Ning Xu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China
| | - Fuquan Zhao
- Hubei Lulingwang Liquor Industry Co., Ltd, Fangxian 442399, Hubei, China
| | - Dongsheng Li
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China
| | - Yong Hu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan, 430068, Hubei, China; Hubei Xizhiyuan Bioengineering Co., Ltd, 445099, Hubei, China.
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2
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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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Liao S, Zhang Z, Yang C, Gardner EM, Peng Y, Xiong Y, Dai S, Deng Y. A chromosome-level genome assembly of Ficus benjamina, a fig tree with great ecological and ornamental value. Sci Data 2025; 12:824. [PMID: 40393990 PMCID: PMC12092655 DOI: 10.1038/s41597-025-05155-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: 12/26/2024] [Accepted: 05/08/2025] [Indexed: 05/22/2025] Open
Abstract
Ficus benjamina, the weeping fig, is one of the most widely distributed and cultivated figs, with important ecological functions and landscape value. However, the lack of a reference genome has hindered molecular and functional research on this well-known fig-tree. Here we present a chromosome-scale genome assembly and annotation for F. benjamina, based on a combination of Illumina short-reads, PacBio subreads, and Hi-C sequencing data. The genome consists of 13 pseudochromosomes that contain 362.73 Mb of assembled sequences, with a contig N50 length of 25.76 Mb and a complete BUSCO score of 98.10%. In total, 28,840 protein-coding genes were identified, of which 96.22% were functionally annotated. Our study provides the first chromosome-level genome of F. benjamina, providing an important resource for exploring the genetic basis of its ecological and horticultural characters.
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Affiliation(s)
- Shuai Liao
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangzhou International Ficus Research Center, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, 510405, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou, 510650, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Zhen Zhang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Chenxuan Yang
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Elliot M Gardner
- Department of Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yanqiong Peng
- State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Yongmei Xiong
- Guangzhou International Ficus Research Center, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, 510405, China
| | - Seping Dai
- Guangzhou International Ficus Research Center, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, 510405, China.
| | - Yunfei Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou, 510650, China.
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Dong WY, Huang TY, Zhao SY, Zhang J, Lei Y, Huang J, Zhou ZS, Lu YB. Chromosome-level genome assembly of the parasitoid wasp Aenasius arizonensis. Sci Data 2025; 12:809. [PMID: 40382346 PMCID: PMC12085690 DOI: 10.1038/s41597-025-05020-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: 12/09/2024] [Accepted: 04/14/2025] [Indexed: 05/20/2025] Open
Abstract
Aenasius arizonensis is an important solitary endoparasitoid successfully used for biocontrol of cotton mealybug. However, lacking genomic resources has limited molecular-level investigations. Our exploration produced a superior genomic assembly of A. arizonensis from the chromosome level by combining MGISEQ short reads, Hi-C scaffolding, and PacBio Revio sequencing techniques. The genome measured 398.69 Mb, including a contig N50 of 4.73 Mb, a BUSCO completeness level of 97.07%, and a scaffold N50 of 35.96 Mb. Hi-C data were further utilized cluster and anchor 98.66% of the genome sequences into 11 chromosomes. Approximately, 165.90 Mb, representing about 41.61% of the genome, was identified as repeat elements. Non-coding sequence annotation identified 171 rRNAs, 117 small RNAs, 331 regulatory RNAs, and 872 tRNAs. Genome annotation reveals 11,727 protein-coding genes, with 10,842 (92.45%) genes functionally annotated. In summary, our chromosome-level genome assembly serves as a significant resource for advancing research on Encyrtidae parasitoids.
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Affiliation(s)
- Wan-Ying Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Tian-Yu Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Sheng-Yuan Zhao
- Institute of Bio-Interaction, Xianghu Laboratory, Hangzhou, 311258, China
| | - Juan Zhang
- Zhejiang Institute of Landscape Plants and Flowers, Zhejiang Xiaoshan Institute of Cotton & Bast Fiber Crops, Hangzhou, 311251, China
| | - Yang Lei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jun Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zhong-Shi Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572019, China.
| | - Yao-Bin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
- Institute of Bio-Interaction, Xianghu Laboratory, Hangzhou, 311258, China.
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Usman S, Xu D, Ma J, Sheoran N, Okoye CO, Guo X. Comparative Genomics Reveals the Molecular Mechanisms of a Newly Isolated Pediococcus cellicola zy165 Strain and Its Adaptation in Corn Silage. Biochem Genet 2025:10.1007/s10528-025-11114-2. [PMID: 40327195 DOI: 10.1007/s10528-025-11114-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2024] [Accepted: 04/20/2025] [Indexed: 05/07/2025]
Abstract
Understanding how lactic acid bacteria (LAB) adapt to the silage environment is crucial for optimizing fermentation processes and developing efficient inoculants. In this study, Pediococcus cellicola zy165, isolated from fermented whole-crop corn, was subjected to whole-genome sequencing and comparative genomic analysis with two reference strains from NCBI (P. cellicola DSM 17757, and P. cellicola NBRC 106103, isolated from distilled-spirit-fermenting cellars), to elucidate its adaptation mechanisms in silage. The genome of P. cellicola zy165, which includes a circular plasmid and a CRISPR element, revealed enrichment in genes linked to carbohydrate metabolism, transport, and regulatory functions. Key adaptations for silage fermentation were evidenced by the presence of diverse phosphotransferase system (PTS) components, facilitating efficient sugar uptake and metabolism, alongside enzymes like phosphoglycerate mutase and L-lactate dehydrogenase, which are pivotal for glycolysis and lactic acid production, respectively. Additionally, the strain's genome encodes for acetate kinase, suggesting a strategic approach to pH management and energy conservation. Unique to P. cellicola zy165, genes encoding alpha-galactosidase and fructoselysine 6-phosphate deglycase were identified, indicating specialized capabilities for carbohydrate degradation in the silage niche. Structural variations and mutation analyses further highlighted adaptive genetic changes, including those in DNA metabolic processes, which could enhance survival under silage conditions. These genomic insights highlight the potential of P. cellicola zy165 as an effective silage inoculant, showcasing its evolutionary adaptations to the anaerobic, nutrient-rich corn silage environment.
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Affiliation(s)
- Samaila Usman
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
- Probiotics and Life Health Institute, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Dongmei Xu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
- Probiotics and Life Health Institute, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jing Ma
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
- Probiotics and Life Health Institute, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Neha Sheoran
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
- Probiotics and Life Health Institute, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Charles Obinwanne Okoye
- Biofuels Institute, School of Environment & Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
- Department of Zoology & Environmental Biology, University of Nigeria, Nsukka, 410001, Nigeria
| | - Xusheng Guo
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
- Probiotics and Life Health Institute, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Wang J, Chen J, Hu Y, Song C, Li X, Qian Y, Deng L. DeepMFFGO: A Protein Function Prediction Method for Large-Scale Multifeature Fusion. J Chem Inf Model 2025; 65:3841-3853. [PMID: 40116538 DOI: 10.1021/acs.jcim.5c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2025]
Abstract
Protein functional studies are crucial in the fields of drug target discovery and drug design. However, the existing methods have significant bottlenecks in utilizing multisource data fusion and Gene Ontology (GO) hierarchy. To this end, this study innovatively proposes the DeepMFFGO model designed for protein function prediction under large-scale multifeature fusion. A fine-tuning strategy using intermediate-level feature selection is proposed to reduce redundancy in protein sequences and mitigate distortion of the top-level features. A hierarchical progressive fusion structure is designed to explore feature connections, optimize complementarity through dynamic weight allocation, and reduce redundant interference. On the CAFA3 data set, the Fmax values of the DeepMFFGO model on the MF, BP, and CC ontologies reach 0.702, 0.599, and 0.704, respectively, which are improved by 4.2%, 2.4%, and 0.07%, respectively, compared with state-of-the-art multisource methods.
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Affiliation(s)
- Jingfu Wang
- School of Software, Xinjiang University, Urumqi 830091, China
- Xinjiang Engineering Research Center of Big Data and Intelligent Software, School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
| | - Jiaying Chen
- School of Software, Xinjiang University, Urumqi 830091, China
- Xinjiang Engineering Research Center of Big Data and Intelligent Software, School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
| | - Yue Hu
- School of Computer Science and Technology, Xinjiang University, Urumqi 830046, China
- Joint International Research Laboratory of Silk Road Multilingual Cognitive Computing, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Chaolin Song
- School of Software, Xinjiang University, Urumqi 830091, China
- Xinjiang Engineering Research Center of Big Data and Intelligent Software, School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
| | - Xinhui Li
- School of Computer Science and Technology, Xinjiang University, Urumqi 830046, China
- Joint International Research Laboratory of Silk Road Multilingual Cognitive Computing, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Yurong Qian
- Xinjiang Engineering Research Center of Big Data and Intelligent Software, School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
- School of Computer Science and Technology, Xinjiang University, Urumqi 830046, China
- Joint International Research Laboratory of Silk Road Multilingual Cognitive Computing, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Lei Deng
- School of Software, Xinjiang University, Urumqi 830091, China
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
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Ma L, Zeng X, Wang J, Xiong H, Yu Y, Liu H, Yang QY, Yang R, Yang X. Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii. Sci Data 2025; 12:597. [PMID: 40210914 PMCID: PMC11985934 DOI: 10.1038/s41597-025-04943-8] [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: 01/15/2025] [Accepted: 04/01/2025] [Indexed: 04/12/2025] Open
Abstract
The genus Triplophysa exhibits remarkable adaptability to the unique environment found at the Qinghai-Tibet Plateau (QTP). Higher quality genomes are helpful to the study of the adaptability to the extreme environment in the plateau. This study utilized PacBio HiFi, Ultra-long ONT, and Hi-C sequencing of Triplophysa yaopeizhii to construct the first telomere-to-telomere (T2T) gapless genome assembly of the genus Triplophysa. The genome size is 671.58 Mb, with a contig N50 length of 26.04 Mb. The sequences were anchored onto 25 chromosomes with all centromeres and telomeres. Furthermore, 293.98 Mb (43.77%) of repetitive sequences and 26,487 protein-coding genes were identified. Comparative analyses with the genomes of closely related species demonstrated high completeness, continuity, and accuracy of the genome. The genomic quality was further substantiated by the QV of 31.82 with 96.60% of BUSCO. This study provides a valuable genetic resource of the genus Triplophysa and serves as an essential reference for elucidating the adaptive genetic mechanisms of plateau fish to the high altitude.
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Affiliation(s)
- Li Ma
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Zeng
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jixiao Wang
- Yebatan Branch of Huadian Jinshajiang Upstream Hydropower Development Co., Ltd., Ganzi, 627153, China
| | - Hao Xiong
- Yebatan Branch of Huadian Jinshajiang Upstream Hydropower Development Co., Ltd., Ganzi, 627153, China
| | - Yongyao Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiping Liu
- College of Fisheries, Southwest University, Chongqing, 402460, China
| | - Qing-Yong Yang
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruibin Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuefen Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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Huang W, Xiang J, Ding Y, Liu W, Fang N, Xiong Y, Dai S, Yu H. A high-quality chromosome-level genome assembly of Antiaris toxicaria. BMC Genom Data 2025; 26:21. [PMID: 40128643 PMCID: PMC11934813 DOI: 10.1186/s12863-025-01309-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Accepted: 03/10/2025] [Indexed: 03/26/2025] Open
Abstract
OBJECTIVES Antiaris toxicaria is a tall tree belonging to the Moraceae family, known for its medicinal value. Its latex contains various cardiac glycosides, which hold significant research and potential application value. However, the lack of genomic resources for A. toxicaria currently hinders molecular genetic studies on its medicinal components. For its effective conservation and elucidation of the distinctive genetic traits of and medical components, we present its chromosome-level genome assembly. DATA DESCRIPTION Here, we assembled two haplotypes of A. toxicaria, including a 671.73-Mb HapA subgenome containing 27,213 genes and a 666.41-Mb HapB subgenome containing 28,840 genes. Their contig N50 sizes were 90.18 and 90.29 Mb, respectively. The transposable elements represented 61.15% and 64.13% of the total assembled genome in HapA and HapB subgenome, respectively. A total of 27,213 and 28,840 genes were predicted in the two haplotypes. Hopefully, this chromosome-level genome of A. toxicaria will provide a valuable resource to enhance understanding of the biosynthesis of medicinal compounds.
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Affiliation(s)
- Weicheng Huang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jiaxin Xiang
- Department of Computer Science, Hong Kong Baptist University, Kowloon, 999077, Hong Kong, China
| | - Yamei Ding
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Wanzhen Liu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ni Fang
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yongmei Xiong
- Guangzhou Institute of Forestry and Landscape Architecture, Guanzhou, 510405, China
| | - Seping Dai
- Guangzhou Institute of Forestry and Landscape Architecture, Guanzhou, 510405, China.
| | - Hui Yu
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, The Chinese Academy of Sciences, Guangzhou, 510650, China.
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.
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9
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Cao J, Tong Y, Xiao Z, Chen H, Liu Z. Chromosome-level genome assembly of Jaguar guapote (Parachromis manguensis) by massive parallel sequencing. Sci Data 2025; 12:411. [PMID: 40064893 PMCID: PMC11894119 DOI: 10.1038/s41597-025-04752-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: 09/11/2024] [Accepted: 03/04/2025] [Indexed: 03/14/2025] Open
Abstract
Parachromis managuensis is a native cichlid fish from Central America and is the most commonly traded species within its genus. This study presents the first chromosome-scale genome assembly of P. managuensis using PacBio HiFi long reads and Hi-C sequencing data. The size of the P. managuensis genome is approximately 896.66 Mb, with a scaffold N50 of 38.19 Mb. The assembled genome demonstrates high quality in terms of completeness and accuracy, with a BUSCO score of 98.85% and a quality value (QV) of 50.95. A total of 888.60 Mb (99.10%) sequences were anchored to 24 pseudochromosomes. Additionally, 21,145 protein-coding genes and 325.58 Mb (~36.31%) repetitive sequences were identified. This chromosome-level genome assembly provides a crucial reference for studying the evolution and ecological adaptability of P. managuensis.
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Affiliation(s)
- Jianmeng Cao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Yannan Tong
- Hainan Academy of Ocean and Fisheries Science, Haikou, 570206, China
| | - Zhigang Xiao
- Menghai County Fisheries Technology Extension Station of Xishuangbanna Dai Autonomous Prefecture, Menghai, 666200, China
| | - Huizi Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Zhigang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
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10
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Liu S, Zheng N, Wang J, Zhao S. Nitrogen metabolism of the highly ureolytic bacterium Proteus penneri S99 isolated from the rumen. BMC Microbiol 2025; 25:104. [PMID: 40021987 PMCID: PMC11869435 DOI: 10.1186/s12866-025-03808-9] [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: 08/13/2024] [Accepted: 02/05/2025] [Indexed: 03/03/2025] Open
Abstract
BACKGROUND The model rumen-dominant ureolytic bacterium P. penneri S99 exhibits high urease activity. It was cultivated using ammonia, urea, amino acids, or their combination as nitrogen sources. To identify differences in gene expression, the transcript abundances of various genes involved in nitrogen metabolism were analyzed by harvesting mRNA from cells during the exponential growth phases on different nitrogen sources. RESULTS P. penneri S99 can utilize ammonia, urea, or amino acids as the sole nitrogen sources for growth and shows a preference for utilizing urea. It exhibits similar growth rates and maximum biomass on ammonia and urea, but showed higher growth rates and maximum biomass on amino acids. Transcriptome sequencing analysis revealed different transcription patterns in response to different nitrogen sources. The urease gene expression was detected in all three different nitrogen sources, and complete hydrolysis of urea was also observed when other nitrogen sources were added to the medium containing urea. The regulation of urease in P. penneri S99 was characterized by constitutive expression, not by urea. The growth of P. penneri S99 on ammonia, ammonium acid, and urea was similar, with the only observed difference being an increase in urease transcript abundance. CONCLUSIONS The transcription patterns of nitrogen metabolism genes offer insights into how nitrogen is utilized in the rumen.
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Affiliation(s)
- Sijia Liu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Nan Zheng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
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11
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Wang W, Kyrkou I, Bojer MS, Kalloubi D, Kali AJ, Alena-Rodriguez M, Leisner JJ, Fulaz S, Ingmer H. Characterization of agr-like Loci in Lactiplantibacillus plantarum and L. paraplantarum and Their Role in Quorum Sensing and Virulence Inhibition of Staphylococcus aureus. Probiotics Antimicrob Proteins 2025:10.1007/s12602-025-10476-8. [PMID: 39966225 DOI: 10.1007/s12602-025-10476-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2025] [Indexed: 02/20/2025]
Abstract
The pathogenicity of Staphylococcus aureus is largely regulated by the agr quorum sensing (QS) system encoded by agrBDCA, which coordinates virulence factor production through secretion and sensing of auto-inducing peptides (AIPs). agr-like systems are also present in coagulase-negative staphylococci, and several of these encode AIPs that inhibit S. aureus QS. In lactic acid bacteria, a similar locus was previously identified in Lactiplantibacillus plantarum WCSF1 termed lamBDCA. Here, we characterized the lamBDCA locus in L. plantarum LMG 13556 and L. paraplantarum CIRM-BIA 1870, and explored the effects on S. aureus QS. Notably, we found that co-cultivation with L. paraplantarum significantly inhibits S. aureus QS and hemolysin production, while less so for L. plantarum. The inhibition by L. paraplantarum was lost upon disruption of its lamBDCA locus, suggesting that the L. paraplantarum AIP mediates cross-species interference with S. aureus agr activation. Transcriptomic analysis revealed that lamBDCA in L. paraplantarum controls the expression of genes belonging to various functional categories, including stress response and metabolism. The latter includes genes encoding riboflavin (B2 vitamin) biosynthesis, which enabled the growth of the L. paraplantarum lamB mutant in the presence of roseoflavin, a toxic riboflavin analogue. Collectively, our results show that L. paraplantarum CIRM-BIA 1870 interferes with S. aureus virulence gene expression through QS suppression, and they implicate QS in the probiotic properties of L. paraplantarum.
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Affiliation(s)
- Weizhe Wang
- Bacterial & Viruses Section, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Copenhagen, Denmark
| | - Ifigeneia Kyrkou
- Bacterial & Viruses Section, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Copenhagen, Denmark
| | - Martin S Bojer
- Bacterial & Viruses Section, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Copenhagen, Denmark
| | - Dina Kalloubi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Abdul Jabbar Kali
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Miguel Alena-Rodriguez
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Jørgen J Leisner
- Bacterial & Viruses Section, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Copenhagen, Denmark
| | - Stephanie Fulaz
- Bacterial & Viruses Section, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Copenhagen, Denmark.
| | - Hanne Ingmer
- Bacterial & Viruses Section, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Copenhagen, Denmark.
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12
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Bian Q, Shen Z, Gao J, Shen L, Lu Y, Zhang Q, Chen R, Xu D, Liu T, Che J, Lu Y, Dong X. PPI-CoAttNet: A Web Server for Protein-Protein Interaction Tasks Using a Coattention Model. J Chem Inf Model 2025; 65:461-471. [PMID: 39761551 DOI: 10.1021/acs.jcim.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Predicting protein-protein interactions (PPIs) is crucial for advancing drug discovery. Despite the proposal of numerous advanced computational methods, these approaches often suffer from poor usability for biologists and lack generalization. In this study, we designed a deep learning model based on a coattention mechanism that was capable of both PPI and site prediction and used this model as the foundation for PPI-CoAttNet, a user-friendly, multifunctional web server for PPI prediction. This platform provides comprehensive services for online PPI model training, PPI and site prediction, and prediction of interactions with proteins associated with highly prevalent cancers. In our Homo sapiens test set for PPI prediction, PPI-CoAttNet achieved an AUC of 0.9841 and an F1 score of 0.9440, outperforming most state-of-the-art models. Additionally, these results are generated in real time, delivering outcomes within minutes. We also evaluated PPI-CoAttNet for downstream tasks, including novel E3 ligase scoring, demonstrating outstanding accuracy. We believe that this tool will empower researchers, especially those without computational expertise, to leverage AI for accelerating drug development.
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Affiliation(s)
- Qingyu Bian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zheyuan Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jian Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Liteng Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yang Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Qingnan Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Roufen Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Donghang Xu
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tao Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jinxin Che
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yan Lu
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaowu Dong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310058, China
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13
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Wang MY, Zhang BL, Liang QQ, Lian XM, Zhang K, Yang QE, Yang WK. Chromosome-level genome assembly, annotation, and population genomic resource of argali (Ovis ammon). Sci Data 2025; 12:57. [PMID: 39799149 PMCID: PMC11724849 DOI: 10.1038/s41597-025-04400-6] [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: 07/19/2024] [Accepted: 01/02/2025] [Indexed: 01/15/2025] Open
Abstract
Argali stands as the largest species among wild sheep in Central and East Asia, with a concerning rate of decline estimated at 30%. The intraspecific taxonomy of argali remains contentious due to limited genomic data and unclear geographic separation. In this study, we constructed a chromosome-level genome assembly and annotation for the Tibetan argali (O. a. hodgsoni), together with population genomic resequencing of 32 individuals representing four subspecies. The contig-level genome was 2.64 Gb in size, with a contig N50 length of 71.69 Mb and an estimated genomic completeness of 96.01%. Using Hi-C sequencing data scaffolding, 99.90% of initially assembled sequences were mapped and oriented onto 28 pseudo-chromosomes except the Y chromosome. Annotation uncovered 21,564 protein-coding genes and 46.38% repeat sequences. The average coverage of the population resequencing data was 23.74 with mean mapping ratio up to of 97.19%. The high-quality genome assembly and annotation of the Tibetan argali, coupled with the high-depth population genomic data, will serve as a valuable genetic resource for studies on the taxonomy and conservation of argali.
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Affiliation(s)
- Mu-Yang Wang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- China-Tajikistan Belt and Road Joint Laboratory on Biodiversity Conservation and Sustainable Use, Urumqi, 830011, China
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Bao-Lin Zhang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, 650223, China
| | - Qi-Qi Liang
- Beijing Bio Huaxing Gene Technology Co., LTDs, Beijing, 100049, China
| | - Xin-Ming Lian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Ke Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China
| | - Qi-En Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, China.
| | - Wei-Kang Yang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- China-Tajikistan Belt and Road Joint Laboratory on Biodiversity Conservation and Sustainable Use, Urumqi, 830011, China.
- Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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14
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Cao C, Miao J, Xie Q, Sun J, Cheng H, Zhang Z, Wu F, Liu S, Ye X, Gong H, Zhang Z, Wang Q, Pan Y, Wang Z. A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research. Gigascience 2025; 14:giaf048. [PMID: 40372724 PMCID: PMC12080228 DOI: 10.1093/gigascience/giaf048] [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: 10/21/2024] [Revised: 01/29/2025] [Accepted: 03/31/2025] [Indexed: 05/16/2025] Open
Abstract
BACKGROUND Pigs are crucial sources of meat and protein, valuable animal models, and potential donors for xenotransplantation. However, the existing reference genome for pigs is incomplete, with thousands of segments and centromeres and telomeres missing, which limits our understanding of the important traits in these genomic regions. FINDINGS We present a near-complete genome assembly for the Jinhua pig (JH-T2T) and provide a set of diploid Jinhua reference genomes, constructed using PacBio HiFi, ONT long reads, and Hi-C reads. This assembly includes all 18 autosomes and the X and Y sex chromosomes, with only 6 gaps. It features annotations of 46.90% repetitive sequences, 33 telomeres, 17 centromeres, and 23,924 high-confident genes. Compared to the Sscrofa11.1, JH-T2T closes nearly all gaps, extends sequences by 177 Mb, predicts more intact telomeres and centromeres, and gains 799 more genes and loses 114 genes. Moreover, it enhances the mapping rate for both Western and Chinese local pigs, outperforming Sscrofa11.1 as a reference genome. Additionally, this comprehensive genome assembly will facilitate large-scale variant detection. CONCLUSIONS This study produced a near-gapless assembly of the pig genome and provides a set of haploid Jinhua reference genomes. Our findings represent a significant advance in pig genomics, providing a robust resource that enhances genetic research, breeding programs, and biomedical applications.
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Affiliation(s)
- Caiyun Cao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Hainan Institute of Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025 Hainan, China
| | - Jian Miao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qinqin Xie
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hong Cheng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhenyang Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fen Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaowei Ye
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huanfa Gong
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Hainan Institute of Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025 Hainan, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Hainan Institute of Zhejiang University, Building 11, Yongyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025 Hainan, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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15
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Cao M, Ding Z, Wang X, Guo S, Kang Y, Hu L, Zhang B, Pei J, Ma Y, Guo X. Full-length transcriptome sequencing of the longissimus dorsi muscle of yak and cattle-yak using nanopore technology. Int J Biol Macromol 2025; 284:138071. [PMID: 39603298 DOI: 10.1016/j.ijbiomac.2024.138071] [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: 09/09/2024] [Revised: 11/13/2024] [Accepted: 11/23/2024] [Indexed: 11/29/2024]
Abstract
Short-read RNA sequencing has been used to sequence the transcriptome of the skeletal muscle of yak and cattle-yak; however, full-length transcripts cannot be obtained and alternative splicing (AS) events cannot be inferred using this sequencing approach. Here, we used Oxford Nanopore Technologies (ONT) full-length sequencing to sequence the transcriptome of the longissimus dorsi of yak and cattle-yak. A total of 20,323 novel genes and 172,870 novel transcripts were identified, and 159,700 novel transcripts were successfully annotated. A total of 157,812 AS events, 58,073 simple sequence repeats, 57,468 complete open reading frames, 2296 transcription factors, and 20,404 lncRNAs were detected. Differentially expressed transcripts (DETs) in the longissimus dorsi muscle of yak and cattle-yak were involved in the MAPK and JAK-STAT signaling pathways related to muscle development and growth. Protein-protein interaction analysis of DETs suggested that TNNI2 might make a major contribution to differences in muscle growth and meat quality traits between yak and cattle-yak. The results have enriched the transcriptome data of dorsal muscles, providing new ideas for the study of transcriptional regulation processes, and also providing useful information for the production of higher yields of yak meat.
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Affiliation(s)
- Mengli Cao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xingdong Wang
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Liyan Hu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ben Zhang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yi Ma
- Tianjin Academy of Agriculture Sciences, Tianjin 300192, China.
| | - Xian Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
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16
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Wang Y, Yang Y, Wu Y, Liu Y, Li Q, Liu C, Jiang Z, Jiang W, Chen F, Mu X. Chromosome-level genome assembly of the ratmouth barbel, Ptychidio jordani. Sci Data 2024; 11:1435. [PMID: 39725708 DOI: 10.1038/s41597-024-04331-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 12/18/2024] [Indexed: 12/28/2024] Open
Abstract
The ratmouth barbel (Ptychidio jordani) is a critically endangered freshwater fish from the Cyprinidae family, primarily due to overfishing and habitat disruption. To address the challenges of its shrinking wild populations and the difficulties in artificial reproduction, we sequenced, assembled, and annotated a high-quality chromosome-level genome of P. jordani using next-generation short-read sequencing, third-generation long-read sequencing, and Hi-C sequencing. The final genome assembly was 1.14 Gb, consisting of 25 chromosomes with a contig N50 of 25.14 Mb and a scaffold N50 of 42.91 Mb. We identified 25,183 protein-coding genes, 751.75 Mb of repeats, and 19,373 ncRNAs. Methylation loci on most chromosomes ranged from 1,000 to 3,000 per 100 kb window. Gene expression levels across various tissues were analyzed, revealing 12,135 (caudal fin), 11,465 (liver), 14,438 (gill), 12,413 (heart), 8,301 (spleen), and 3,578 (kidney) differentially expressed genes compared to muscle. The comprehensive genomic and transcriptomic resources generated here will aid in understanding the ecology, adaptation, and environmental responses of P. jordani, supporting future research and conservation efforts.
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Affiliation(s)
- Yuanyuan Wang
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Yexin Yang
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Yuli Wu
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, 510520, China
| | - Yi Liu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Qingyong Li
- Fisheries Research and Extension Center of Huizhou, Huizhou, China
| | - Chao Liu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Zhiyong Jiang
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, 510520, China
| | - Wanying Jiang
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, 510520, China
| | - Fangcan Chen
- Guangdong Hanyu ecological technology co., LtD, Guangzhou, China
| | - Xidong Mu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Immunology and Sustainable Aquaculture, Guangzhou, 510380, China.
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17
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Wu J, Liu Y, Zhu Y, Yu DJ. Improving Antifreeze Proteins Prediction With Protein Language Models and Hybrid Feature Extraction Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024; 21:2349-2358. [PMID: 39316498 DOI: 10.1109/tcbb.2024.3467261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Accurate identification of antifreeze proteins (AFPs) is crucial in developing biomimetic synthetic anti-icing materials and low-temperature organ preservation materials. Although numerous machine learning-based methods have been proposed for AFPs prediction, the complex and diverse nature of AFPs limits the prediction performance of existing methods. In this study, we propose AFP-Deep, a new deep learning method to predict antifreeze proteins by integrating embedding from protein sequences with pre-trained protein language models and evolutionary contexts with hybrid feature extraction networks. The experimental results demonstrated that the main advantage of AFP-Deep is its utilization of pre-trained protein language models, which can extract discriminative global contextual features from protein sequences. Additionally, the hybrid deep neural networks designed for protein language models and evolutionary context feature extraction enhance the correlation between embeddings and antifreeze pattern. The performance evaluation results show that AFP-Deep achieves superior performance compared to state-of-the-art models on benchmark datasets, achieving an AUPRC of 0.724 and 0.924, respectively.
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18
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Feng J, Zhang W, Chen C, Liang Y, Li T, Wu Y, Liu H, Wu J, Lin W, Li J, He Y, He J, Luan A. The pineapple reference genome: Telomere-to-telomere assembly, manually curated annotation, and comparative analysis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:2208-2225. [PMID: 39109967 DOI: 10.1111/jipb.13748] [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: 12/21/2023] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 10/19/2024]
Abstract
Pineapple is the third most crucial tropical fruit worldwide and available in five varieties. Genomes of different pineapple varieties have been released to date; however, none of them are complete, with all exhibiting substantial gaps and representing only two of the five pineapple varieties. This significantly hinders the advancement of pineapple breeding efforts. In this study, we sequenced the genomes of three varieties: a wild pineapple variety, a fiber pineapple variety, and a globally cultivated edible pineapple variety. We constructed the first gap-free reference genome (Ref) for pineapple. By consolidating multiple sources of evidence and manually revising each gene structure annotation, we identified 26,656 protein-coding genes. The BUSCO evaluation indicated a completeness of 99.2%, demonstrating the high quality of the gene structure annotations in this genome. Utilizing these resources, we identified 7,209 structural variations across the three varieties. Approximately 30.8% of pineapple genes were located within ±5 kb of structural variations, including 30 genes associated with anthocyanin synthesis. Further analysis and functional experiments demonstrated that the high expression of AcMYB528 aligns with the accumulation of anthocyanins in the leaves, both of which may be affected by a 1.9-kb insertion fragment. In addition, we developed the Ananas Genome Database, which offers data browsing, retrieval, analysis, and download functions. The construction of this database addresses the lack of pineapple genome resource databases. In summary, we acquired a seamless pineapple reference genome with high-quality gene structure annotations, providing a solid foundation for pineapple genomics and a valuable reference for pineapple breeding.
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Affiliation(s)
- Junting Feng
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- National Key Laboratory for Tropical Crop Breeding, Sanya Research Institute, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 572024, China
| | - Wei Zhang
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Chengjie Chen
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yinlong Liang
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Tangxiu Li
- Nanfan Research Institute of Hainan University, Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Tropical Agriculture and Forestry, Hainan University, Sanya, 572025, China
| | - Ya Wu
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Wu
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wenqiu Lin
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091, China
| | - Jiawei Li
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yehua He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Junhu He
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Aiping Luan
- National Key Laboratory for Tropical Crop Breeding, Laboratory of Crop Gene Resources and Germplasm Enhancement in South China, Ministry of Agriculture and Rural Affairs, Key Laboratory of Tropical Crops Germplasm Resources Genetic Improvement and Innovation of Hainan Province, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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19
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Wu L, Gu S, Wen P, Wu L, Li L, Guo S, Ding S. Chromosome-level genome assembly and annotation of the Spinibarbus caldwelli. Sci Data 2024; 11:933. [PMID: 39198473 PMCID: PMC11358287 DOI: 10.1038/s41597-024-03796-x] [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: 05/24/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
Spinibarbus caldwelli is an important freshwater economic fish in China. Owing to uncontrolled fishing, wild resources of S. caldwelli have decreased rapidly and may be on the verge of extinction. In this study, utilizing single-molecule real-time (SMRT) sequencing technology and chromatin interaction mapping (Hi-C) technologies, we assembled the first chromosome-scale genome for S. caldwelli about 1.77 Gb in size, with a contig N50 length of 11.83 Mb and scaffold N50 length of 33.91 Mb. In total 1.72 Gb (97.01%) of the contig sequences were anchored onto fifty chromosomes with the longest scaffold being 56.20 Mb. Furthermore, proximately 49.41% of the genome was composed of repetitive elements. In total, 49,377 protein-coding genes were predicted, of which 47,724 (96.65%) genes have been functionally annotated. The high-quality chromosome-level reference genome and annotation are vital for supporting basic genetic studies and will be contribute to genetic structure, functional elucidation, evolutionary inquiry, and germplasm conservation for S. caldwelli.
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Affiliation(s)
- Lina Wu
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Sui Gu
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ping Wen
- Key laboratory of Cultivation and High - value Utilization of Marine Organisms in Fujian Province Fisheries Research institute of Fujian, Xiamen, 361013, China
| | - Lisheng Wu
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Leibin Li
- Key laboratory of Cultivation and High - value Utilization of Marine Organisms in Fujian Province Fisheries Research institute of Fujian, Xiamen, 361013, China
| | - Shaopeng Guo
- Key laboratory of Cultivation and High - value Utilization of Marine Organisms in Fujian Province Fisheries Research institute of Fujian, Xiamen, 361013, China
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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20
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Tadesse BT, Gu L, Solem C, Mijakovic I, Jers C. The Probiotic Enterococcus Lactis SF68 as a Potential Food Fermentation Microorganism for Safe Food Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18089-18099. [PMID: 39102436 DOI: 10.1021/acs.jafc.4c03644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Due to the reports describing virulent and multidrug resistant enterococci, their use has become a topic of controversy despite most of them being safe and commonly used in traditionally fermented foods worldwide. We have characterized Enterococcus lactis SF68, a probiotic strain approved by the European Food Safety Authority (EFSA) for use in food and feed, and find that it has a remarkable potential in food fermentations. Genome analysis revealed the potential of SF68 to metabolize a multitude of carbohydrates, including lactose and sucrose, which was substantiated experimentally. Bacteriocin biosynthesis clusters were identified and SF68 was found to display a strong inhibitory effect against Listeria monocytogenes. Fermentation-wise, E. lactis SF68 was remarkably like Lactococcus lactis and displayed a clear mixed-acid shift on slowly fermented sugars. SF68 could produce the butter aroma compounds, acetoin and diacetyl, the production of which was enhanced under aerated conditions in a strain deficient in lactate dehydrogenase activity. Overall, E. lactis SF68 was found to be versatile, with a broad carbohydrate utilization capacity, a capacity for producing bacteriocins, and an ability to grow at elevated temperatures. This is key to eliminating pathogenic and spoilage microorganisms that are frequently associated with fermented foods.
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Affiliation(s)
- Belay Tilahun Tadesse
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Lyngby 2800, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Lyngby 2800, Denmark
| | - Liuyan Gu
- Department of Bio- and Chemical Engineering, Aarhus University, Gustav Wieds vej 10, Aarhus 8000, Denmark
| | - Christian Solem
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Lyngby 2800, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Lyngby 2800, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Lyngby 2800, Denmark
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21
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Duan M, Yang S, Li X, Tang X, Cheng Y, Luo J, Wang J, Song H, Wang Q, Zhu GX. Chromosome-level genome assembly and annotation of the Rhabdophis nuchalis (Hubei keelback). Sci Data 2024; 11:850. [PMID: 39117633 PMCID: PMC11310211 DOI: 10.1038/s41597-024-03708-z] [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: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Rhabdophis nuchalis, a snake widely distributed in China, possesses a unique trait: glands beneath the skin on its neck and back, known as nucho-dorsal glands. These features make it a valuable subject for studying genetic diversity and the evolution of complex traits. In this study, we obtained a high-quality chromosome-level reference genome of R. nuchalis using MGI short-read sequencing, PacBio Revio long-read sequencing, and Hi-C sequencing techniques. The final assembly comprised 1.92 Gb of the R. nuchalis genome, anchored to 20 chromosomes (including 9 macrochromosomes and 11 microchromosomes), with a contig N50 of 104.79 Mb, a scaffold N50 of 204.96 Mb, and a BUSCO completeness of 97.50%. Additionally, we annotated a total of 1.09 Gb of repetitive sequences (which constitute 56.51% of the entire genome) and identified 22,057 protein-coding genes. This high-quality reference genome of R. nuchalis furnishes essential genomic data for comprehending the genetic diversity and evolutionary history of the species, as well as for facilitating species conservation efforts and comparative genomics studies.
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Affiliation(s)
- Mingwen Duan
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xiufeng Li
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xuemei Tang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yuqi Cheng
- Chengdu Zoo, Chengdu, Sichuan Province, 610081, China
| | - Jingxue Luo
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ji Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Huina Song
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Guang Xiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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22
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Li M, Chen C, Wang H, Qin H, Hou S, Yang X, Jian J, Gao P, Liu M, Mu Z. Telomere-to-telomere genome assembly of sorghum. Sci Data 2024; 11:835. [PMID: 39095379 PMCID: PMC11297213 DOI: 10.1038/s41597-024-03664-8] [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: 11/28/2023] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
"Cuohu Bazi" (CHBZ) is an ancient sorghum variety collected from the fields of China, known for its agronomic traits like dwarf stature, early maturation. In this study, we present the first telomere-to-telomere (T2T) and gap-free genome assembly of CHBZ using PacBio HiFi reads, Oxford Nanopore Technologies, and Hi-C data. The assembled genome comprises 724.85 Mb, effectively resolving all 3,913 gaps that were present in the previous sorghum BTx623 reference genome. Notably, the T2T assembly captures 10 centromeres and all 20 telomeres, providing strong support for their integrity. This assembly is of high quality in terms of contiguity (contig N50: 71.1 Mb), completeness (BUSCO score: 99.01%, k-mer completeness: 98.88%), and correctness (QV: 61.60). Repetitive sequences accounted for 70.41% of the genome and a total of 32,855 protein-coding genes have been annotated. Furthermore, 161 CHBZ-specific presence/absence variants genes have been identified when comparing to BTx623 genome. This study provides valuable insights for future research on sorghum genetics, genomics, and evolutionary history.
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Affiliation(s)
- Meng Li
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
| | | | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Huibin Qin
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Sen Hou
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | | | | | | | - Minxuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhixin Mu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
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23
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Xiong L, Yu H, Zeng K, Li Y, Wei Y, Li H, Ji X. Whole genome analysis of Pseudomonas mandelii SW-3 and the insights into low-temperature adaptation. Folia Microbiol (Praha) 2024; 69:775-787. [PMID: 38051419 DOI: 10.1007/s12223-023-01117-0] [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: 04/14/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023]
Abstract
Pseudomonas mandelii SW-3, isolated from the Napahai plateau wetland, can survive in cold environments. The mechanisms underlying the survival of bacteria in low temperatures and high altitudes are not yet fully understood. In this study, the whole genome of SW-3 was sequenced to identify the genomic features that may contribute to survival in cold environments. The results showed that the genome size of strain SW-3 was 6,538,059 bp with a GC content of 59%. A total of 67 tRNAs, a 34,110 bp prophage sequence, and a large number of metabolic genes were found. Based on 16S rRNA gene phylogeny and average nucleotide identity analysis among P. mandelii, SW-3 was identified as a strain belonging to P. mandelii. In addition, we clarified the mechanisms by which SW-3 survived in a cold environment, providing a basis for further investigation of host-phage interaction. P. mandelii SW-3 showed stress resistance mechanisms, including glycogen and trehalose metabolic pathways, and antisense transcriptional silencing. Furthermore, cold shock proteins and glucose 6-phosphate dehydrogenase may play pivotal roles in facilitating adaptation to cold environmental conditions. The genome-wide analysis provided us with a deeper understanding of the cold-adapted bacterium.
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Affiliation(s)
- Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Kun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China.
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24
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Huang X, Hu X, Liu Q, Xie Z, Tan S, Qin X, Chen T, Wu W, Saud S, Nawaz T, El-Kahtany K, Fahad S, Yi K. Full-length agave transcriptome reveals candidate glycosyltransferase genes involved in hemicellulose biosynthesis. Int J Biol Macromol 2024; 274:133508. [PMID: 38944067 DOI: 10.1016/j.ijbiomac.2024.133508] [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: 01/27/2024] [Revised: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Agave species are typical crassulacean acid metabolism (CAM) plants commonly cultivated to produce beverages, fibers, and medicines. To date, few studies have examined hemicellulose biosynthesis in Agave H11648, which is the primary cultivar used for fiber production. We conducted PacBio sequencing to obtain full-length transcriptome of five agave tissues: leaves, shoots, roots, flowers, and fruits. A total of 41,807 genes were generated, with a mean length of 2394 bp and an annotation rate of 97.12 % using public databases. We identified 42 glycosyltransferase genes related to hemicellulose biosynthesis, including mixed-linkage glucan (1), glucomannan (5), xyloglucan (16), and xylan (20). Their expression patterns were examined during leaf development and fungal infection, together with hemicellulose content. The results revealed four candidate glycosyltransferase genes involved in xyloglucan and xylan biosynthesis, including glucan synthase (CSLC), xylosyl transferase (XXT), xylan glucuronyltransferase (GUX), and xylan α-1,3-arabinosyltransferase (XAT). These genes can be potential targets for manipulating xyloglucan and xylan traits in agaves, and can also be used as candidate enzymatic tools for enzyme engineering. We have provided the first full-length transcriptome of agave, which will be a useful resource for gene identification and characterization in agave species. We also elucidated the hemicellulose biosynthesis machinery, which will benefit future studies on hemicellulose traits in agave.
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Affiliation(s)
- Xing Huang
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoli Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Zhouli Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shibei Tan
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Weihuai Wu
- National Key Laboratory for Tropical Crop Breeding, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Shah Saud
- College of Life Science, Linyi University, Linyi, Shandong 276000, China
| | - Taufiq Nawaz
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Khaled El-Kahtany
- Geology and Geophysics Department, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Shah Fahad
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; Department of Agronomy, Abdul Wali Khan University Mardan, Khyber Pakh-tunkhwa, 23200, Pakistan.
| | - Kexian Yi
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China; Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China; Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China.
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25
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You X, Fang Q, Chen C, Cao J, Fu S, Zhang T, Wang S, He X, He J, Zhou Y, Wang B, Wang L, Wang Z, Sun T, Yang X, Te R, Jian J, Zhou H, Dai Y, Liu Y. A near complete genome assembly of the East Friesian sheep genome. Sci Data 2024; 11:762. [PMID: 38992134 PMCID: PMC11239650 DOI: 10.1038/s41597-024-03581-w] [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: 11/10/2023] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
Advancements in sequencing have enabled the assembly of numerous sheep genomes, significantly advancing our understanding of the link between genetic variation and phenotypic traits. However, the genome of East Friesian sheep (Ostfriesisches Milchschaf), a key high-yield milk breed, remains to be fully assembled. Here, we constructed a near-complete and gap-free East Friesian genome assembly using PacBio HiFi, ultra-long ONT and Hi-C sequencing. The resulting genome assembly spans approximately 2.96 Gb, with a contig N50 length of 104.1 Mb and only 164 unplaced sequences. Remarkably, our assembly has captured 41 telomeres and 24 centromeres. The assembled sequence is of high quality on completeness (BUSCO score: 97.1%) and correctness (QV: 69.1). In addition, a total of 24,580 protein-coding genes were predicted, of which 97.2% (23,891) carried at least one conserved functional domain. Collectively, this assembly provides not only a near T2T gap-free genome, but also provides a valuable genetic resource for comparative genome studies of sheep and will serve as an important tool for the sheep research community.
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Affiliation(s)
| | | | | | - Junwei Cao
- Inner Mongolia Agricultural University, Hohhot, China
| | - Shaoyin Fu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Teng Zhang
- Inner Mongolia University, Hohhot, China
| | - Shenyuan Wang
- Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolong He
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Jiangfeng He
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Yang Zhou
- Inner Mongolia University, Hohhot, China
| | - Biao Wang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Liwei Wang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Zheng Wang
- Inner Mongolia University, Hohhot, China
| | | | | | - Rigele Te
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | | | - Huanmin Zhou
- Inner Mongolia University, Hohhot, China.
- Inner Mongolia Agricultural University, Hohhot, China.
| | | | - Yongbin Liu
- Inner Mongolia University, Hohhot, China.
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China.
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26
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Ahmed MH, Samia NSN, Singh G, Gupta V, Mishal MFM, Hossain A, Suman KH, Raza A, Dutta AK, Labony MA, Sultana J, Faysal EH, Alnasser SM, Alam P, Azam F. An immuno-informatics approach for annotation of hypothetical proteins and multi-epitope vaccine designed against the Mpox virus. J Biomol Struct Dyn 2024; 42:5288-5307. [PMID: 37519185 DOI: 10.1080/07391102.2023.2239921] [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: 04/02/2023] [Accepted: 06/09/2023] [Indexed: 08/01/2023]
Abstract
A worrying new outbreak of Monkeypox (Mpox) in humans is caused by the Mpox virus (MpoxV). The pathogen has roughly 28 hypothetical proteins of unknown structure, function, and pathogenicity. Using reliable bioinformatics tools, we attempted to analyze the MpoxV genome, identify the role of hypothetical proteins (HPs), and design a potential candidate vaccine. Out of 28, we identified seven hypothetical proteins using multi-server validation with high confidence for the occurrence of conserved domains. Their physical, chemical, and functional characterizations, including molecular weight, theoretical isoelectric point, 3D structures, GRAVY value, subcellular localization, functional motifs, antigenicity, and virulence factors, were performed. We predicted possible cytotoxic T cell (CTL), helper T cell (HTL) and linear and conformational B cell epitopes, which were combined in a 219 amino acid multiepitope vaccine with human β defensin as a linker. This multi-epitopic vaccine was structurally modelled and docked with toll-like receptor-3 (TLR-3). The dynamical stability of the vaccine-TLR-3 docked complexes exhibited stable interactions based on RMSD and RMSF tests. Additionally, the modelled vaccine was cloned in-silico in an E. coli host to check the appropriate expression of the final vaccine built. Our results might conform to an immunogenic and safe vaccine, which would require further experimental validation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Hridoy Ahmed
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh
| | - Nure Sharaf Nower Samia
- Department of Life Sciences (DLS), School of Environment and Life Sciences (SELS), Independent University, Dhaka, Bangladesh
| | - Gagandeep Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi CCRAS, Ministry of Ayush, India
| | - Vandana Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, New Delhi, India
| | | | - Alomgir Hossain
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Adnan Raza
- Bioscience department, COMSATS University of Islamabad, Islamabad, Pakistan
| | - Amit Kumar Dutta
- Department of Microbiology, University of Rajshahi, Rajshahi, Bangladesh
| | - Moriom Akhter Labony
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh
| | - Jakia Sultana
- Department of Botany, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Sulaiman Mohammed Alnasser
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Buraydah, Saudi Arabia
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Niu Y, Fan X, Yang Y, Li J, Lian J, Wang L, Zhang Y, Tang Y, Tang Z. Haplotype-resolved assembly of a pig genome using single-sperm sequencing. Commun Biol 2024; 7:738. [PMID: 38890535 PMCID: PMC11189477 DOI: 10.1038/s42003-024-06397-x] [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: 10/07/2023] [Accepted: 05/29/2024] [Indexed: 06/20/2024] Open
Abstract
Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was developed based on long-read sequencing and sperm-phased markers. The chromosome-level phased assembly showed higher phasing accuracy than methods that rely only on HiFi reads. The use of single-sperm sequencing data enabled the construction of a genetic map, successfully mapping the sperm motility trait to a specific region on chromosome 1 (105.40-110.70 Mb). Furthermore, with the assistance of Y chromosome-bearing sperm data, 26.16 Mb Y chromosome sequences were assembled. We report a reliable approach for assembling chromosome-level phased genomes and reveal the potential of sperm population in basic biology research and sperm phenotype research.
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Affiliation(s)
- Yongchao Niu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiang Li
- Biozeron Shenzhen, Inc., Shenzhen, China
| | | | - Liu Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
| | - Yongjin Zhang
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China.
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Bavadi M, Zhu Z, Zhang B. Evaluation of surfactant-aided polycyclic aromatic hydrocarbon biodegradation by molecular docking and molecular dynamic simulation in the marine environment. CHEMOSPHERE 2024; 358:142171. [PMID: 38714247 DOI: 10.1016/j.chemosphere.2024.142171] [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: 08/02/2023] [Revised: 03/27/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
Marine oil spills directly cause polycyclic aromatic hydrocarbons (PAHs) pollution and affect marine organisms due to their toxic property. Chemical and bio-based dispersants composed of surfactants and solvents are considered effective oil spill-treating agents. Dispersants enhance oil biodegradation in the marine environment by rapidly increasing their solubility in the water column. However, the effect of dispersants, especially surfactants, on PAHs degradation by enzymes produced by microorganisms has not been studied at the molecular level. The role of the cytochrome P450 (CYP) enzyme in converting contaminants into reactive metabolites during the biodegradation process has been evidenced, but the activity in the presence of surfactants is still ambiguous. Thus, this study focused on the evaluation of the impact of chemical and bio-surfactants (i.e., Tween 80 (TWE) and Surfactin (SUC)) on the biodegradation of naphthalene (NAP), chrysene (CHR), and pyrene (PYR), the representative components of PAHs, with CYP enzyme from microalgae Parachlorella kessleri using molecular docking and molecular dynamics (MD) simulation. The molecular docking analysis revealed that PAHs bound to residues at the CYP active site through hydrophobic interactions for biodegradation. The MD simulation showed that the surfactant addition changed the enzyme conformation in the CYP-PAH complexes to provide more interactions between the enzyme and PAHs. This led to an increase in the enzyme's capability to degrade PAHs. Binding free energy (ΔGBind) calculations confirmed that surfactant treatment could enhance PAHs degradation by the enzyme. The SUC gave a better result on NAP and PYR biodegradation based on ΔGBind, while TWE facilitated the biodegradation of CHR. The research outputs could greatly facilitate evaluating the behaviors of oil spill-treating agents and oil spill response operations in the marine environment.
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Affiliation(s)
- Masoumeh Bavadi
- Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, A1B 3X5, Canada
| | - Zhiwen Zhu
- Oceans Science, Fisheries and Oceans Canada, Ottawa, ON, K1A 0E6, Canada
| | - Baiyu Zhang
- Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, A1B 3X5, Canada.
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Huang W, Ding Y, Fan S, Liu W, Chen H, Segar S, Compton SG, Yu H. A high-quality chromosome-level genome assembly of Ficus hirta. Sci Data 2024; 11:526. [PMID: 38778063 PMCID: PMC11111794 DOI: 10.1038/s41597-024-03376-z] [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: 11/30/2023] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Ficus species (Moraceae) play pivotal roles in tropical and subtropical ecosystems. Thriving across diverse habitats, from rainforests to deserts, they harbor a multitude of mutualistic and antagonistic interactions with insects, nematodes, and pathogens. Despite their ecological significance, knowledge about the genomic background of Ficus remains limited. In this study, we report a chromosome-level reference genome of F. hirta, with a total size of 297.27 Mb, containing 28,625 protein-coding genes and 44.67% repeat sequences. These findings illuminate the genetic basis of Ficus responses to environmental challenges, offering valuable genomic resources for understanding genome size, adaptive evolution, and co-evolution with natural enemies and mutualists within the genus.
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Affiliation(s)
- Weicheng Huang
- Plant Resources Conservation and Sustainable Utilization, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yamei Ding
- Plant Resources Conservation and Sustainable Utilization, the Chinese Academy of Sciences, Guangzhou, 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Songle Fan
- Plant Resources Conservation and Sustainable Utilization, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Wanzhen Liu
- Plant Resources Conservation and Sustainable Utilization, the Chinese Academy of Sciences, Guangzhou, 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hongfeng Chen
- Plant Resources Conservation and Sustainable Utilization, the Chinese Academy of Sciences, Guangzhou, 510650, China
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Simon Segar
- Department of Crop and Environment Sciences, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | | | - Hui Yu
- Plant Resources Conservation and Sustainable Utilization, the Chinese Academy of Sciences, Guangzhou, 510650, China.
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China.
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China.
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30
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Chu H, Liu T. Comprehensive Research on Druggable Proteins: From PSSM to Pre-Trained Language Models. Int J Mol Sci 2024; 25:4507. [PMID: 38674091 PMCID: PMC11049818 DOI: 10.3390/ijms25084507] [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: 03/21/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Identification of druggable proteins can greatly reduce the cost of discovering new potential drugs. Traditional experimental approaches to exploring these proteins are often costly, slow, and labor-intensive, making them impractical for large-scale research. In response, recent decades have seen a rise in computational methods. These alternatives support drug discovery by creating advanced predictive models. In this study, we proposed a fast and precise classifier for the identification of druggable proteins using a protein language model (PLM) with fine-tuned evolutionary scale modeling 2 (ESM-2) embeddings, achieving 95.11% accuracy on the benchmark dataset. Furthermore, we made a careful comparison to examine the predictive abilities of ESM-2 embeddings and position-specific scoring matrix (PSSM) features by using the same classifiers. The results suggest that ESM-2 embeddings outperformed PSSM features in terms of accuracy and efficiency. Recognizing the potential of language models, we also developed an end-to-end model based on the generative pre-trained transformers 2 (GPT-2) with modifications. To our knowledge, this is the first time a large language model (LLM) GPT-2 has been deployed for the recognition of druggable proteins. Additionally, a more up-to-date dataset, known as Pharos, was adopted to further validate the performance of the proposed model.
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Affiliation(s)
| | - Taigang Liu
- College of Information Technology, Shanghai Ocean University, Shanghai 201306, China;
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31
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Zhang W, Yang Y, Hua S, Ruan Q, Li D, Wang L, Wang X, Wen X, Liu X, Meng Z. Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara. Sci Data 2024; 11:151. [PMID: 38296995 PMCID: PMC10830450 DOI: 10.1038/s41597-024-02989-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Epinephelus awoara, as known as yellow grouper, is a significant economic marine fish that has been bred artificially in China. However, the genetic structure and evolutionary history of yellow grouper remains largely unknown. Here, this work presents the high-quality chromosome-level genome assembly of yellow grouper using PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The 984.48 Mb chromosome-level genome of yellow grouper was assembled, with a contig N50 length of 39.77 Mb and scaffold N50 length of 41.39 Mb. Approximately 99.76% of assembled sequences were anchored into 24 pseudo-chromosomes with the assistance of Hi-C reads. Furthermore, approximately 41.17% of the genome was composed of repetitive elements. In total, 24,541 protein-coding genes were predicted, of which 22,509 (91.72%) genes were functionally annotated. The highly accurate, chromosome-level reference genome assembly and annotation are crucial to the understanding of population genetic structure, adaptive evolution and speciation of the yellow grouper.
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Affiliation(s)
- Weiwei Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Key Laboratory of Tropical Marine Fish Germplasm Innovation and Utilization, Ministry of Agriculture and Rural Affairs, Sanya, 570000, China
- Hainan Engineering Research Center for Germplasm Innovation and Utilization, Sanya, 570000, China
| | - Sijie Hua
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qingxin Ruan
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Duo Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Le Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore City, 119077, Singapore
| | - Xi Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xin Wen
- School of Marine Biology and Fisheries, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou, 570228, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, 519000, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Southern Laboratory of Ocean Science and Engineering (Zhuhai), Zhuhai, 519000, China.
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Khelghatibana F, Javan-Nikkhah M, Safaie N, Sobhani A, Shams S, Sari E. A reference transcriptome for walnut anthracnose pathogen, Ophiognomonia leptostyla, guides the discovery of candidate virulence genes. Fungal Genet Biol 2023; 169:103828. [PMID: 37657751 DOI: 10.1016/j.fgb.2023.103828] [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: 04/12/2023] [Revised: 08/13/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Despite the economic losses due to the walnut anthracnose, Ophiognomonia leptostyla is an orphan fungus with respect to genomic resources. In the present study, the transcriptome of O. leptostyla was assembled for the first time. RNA sequencing was conducted for the fungal mycelia grown in a liquid media, and the inoculated leaf samples of walnut with the fungal conidia sampled at 48, 96 and 144 h post inoculation (hpi). The completeness, correctness, and contiguity of the de novo transcriptome assemblies generated with Trinity, Oases, SOAPdenovo-Trans and Bridger were compared to identify a single superior reference assembly. In most of the assessment criteria including N50, Transrate score, number of ORFs with known description in gene bank, the percentage of reads mapped back to the transcript (RMBT), BUSCO score, Swiss-Prot coverage bin and RESM-EVAL score, the Bridger assembly was the superior and thus used as a reference for profiling the O. leptostyla transcriptome in liquid media vs. during walnut infection. The k-means clustering of transcripts resulted in four distinct transcription patterns across the three sampling time points. Most of the detected CAZy transcripts had elevated transcription at 96 hpi that is hypothetically concurrent with the start of intracellular growth. The in-silico analysis revealed 103 candidate effectors of which six were members of Necrosis and Ethylene Inducing Like Protein (NLP) gene family belonging to three distinct k-means clusters. This study provided a complex and temporal pattern of the CAZys and candidate effectors transcription during six days post O. leptostyla inoculation on walnut leaves, introducing a list of candidate virulence genes for validation in future studies.
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Affiliation(s)
- Fatemeh Khelghatibana
- Department of Plant Pathology, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran.
| | - Mohammad Javan-Nikkhah
- Department of Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Naser Safaie
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ahmad Sobhani
- Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Somayeh Shams
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, University of Lorestan, Khorramabad, Iran
| | - Ehsan Sari
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
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Wei XY, Jia PP, Hu H, Liu L, Li TY, Li YZ, Pei DS. Multi-omics reveal mechanisms underlying chronic kidney disease of unknown etiology (CKDu) pathogenesis using zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122524. [PMID: 37683759 DOI: 10.1016/j.envpol.2023.122524] [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: 07/24/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Chronic kidney disease of unknown etiology (CKDu) is an endemic disease in the dry zone of farming communities, Sri Lanka. The drinking water in a CKDu prevalent area contains a high concentration of F-, hardness and other environmental pollutants, including heavy metals and microcystin, which are considered possible etiology of CKDu in these areas. Here, multi-omics data with host transcriptome, metabolome and gut microbiomes were obtained using simulated local drinking water of Sri Lanka after their exposure to adult zebrafish. Based on an integrated multi-omics analysis in the context of host physiology in the kidney injury samples with different pathologic grades, two common pathways necroptosis and purine metabolism were identified as potentially important pathways that affect kidney injury. The key metabolite acetyl adenylate in the purine metabolism pathway was significantly positively correlated with Comamonas (rho = 0.72) and significantly negatively correlated with Plesiomonas (rho = -0.58). This crucial metabolite and two key gut bacteria genera may not only be potential markers but also potential therapeutic targets in the uric acid metabolic pathway, which is an important factor in the pathogenesis of acute kidney injury (AKI) in general, as well as of chronic kidney disease (CKD). Based on this, we revealed the urea metabolism pathway of kidney injury in zebrafish and provided a new avenue for the treatment of CKDu in Sri Lanka.
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Affiliation(s)
- Xing-Yi Wei
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China
| | - Huan Hu
- Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Li Liu
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Tian-Yun Li
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yong-Zhi Li
- Chongqing Institute of Green and Intelligent Technology, Chongqing School of University of Chinese Academy of Sciences, Chinese Academy of Sciences, Chongqing, 400714, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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Zhao D, Zhang Y, Ren H, Shi Y, Dong D, Li Z, Cui G, Shen Y, Mou Z, Kennelly EJ, Huang L, Ruan J, Chen S, Yu D, Cun Y. Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2320-2335. [PMID: 37688324 DOI: 10.1111/jipb.13565] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023]
Abstract
Diterpenoid alkaloids (DAs) have been often utilized in clinical practice due to their analgesic and anti-inflammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains unknown. In this study, we successfully assembled a high-quality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum (A. vilmorinianum) (5.76 Gb). An A. vilmorinianum-specific whole-genome duplication event was discovered using comparative genomic analysis, which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in A. vilmorinianum as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.
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Affiliation(s)
- Dake Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Ya Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Huanxing Ren
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yana Shi
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Ding Dong
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Zonghang Li
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Guanghong Cui
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yong Shen
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Zongmin Mou
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Edward J Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, 10468, New York, USA
- Graduate Center, City University of New York, Bronx, 10468, New York, USA
| | - Luqi Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jue Ruan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Suiyun Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, 650500, China
| | - Yupeng Cun
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Zhou Y, Zhang X, Tang X, Zhou Y, Ding Y, Liu H. Chromosome-Level Genome Assembly of Protosalanx chinensis and Response to Air Exposure Stress. BIOLOGY 2023; 12:1266. [PMID: 37759664 PMCID: PMC10525151 DOI: 10.3390/biology12091266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Protosalanx chinensis is a suitable particular species for genetic studies on nearly scaleless skin, transparency and high sensitivity to hypoxia stress. Here, we generated a high-quality chromosome-level de novo assembly of P. chinensis. The final de novo assembly yielded 379.47 Mb with 28 pseudo-chromosomes and a scaffold N50 length of 14.52 Mb. In total, 21,074 protein-coding genes were predicted. P. chinensis, Esox lucius and Hypomesus transpacificus had formed a clade, which diverged about 115.5 million years ago. In the air exposure stress experiment, we found that some genes play an essential role during P. chinensis hypoxia, such as bhlh, Cry1, Clock, Arntl and Rorb in the circadian rhythm pathway. These genomic data offer a crucial foundation for P. chinensis ecology and adaptation studies, as well as a deeper understanding of the response to air exposure stress.
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Affiliation(s)
- Yanfeng Zhou
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China;
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Xizhao Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China;
| | - Xuemei Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Yifan Zhou
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Yuting Ding
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Hong Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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Zhang W, Wang SC, Li Y. Molecular mechanism of thiamine in mitigating drought stress in Chinese wingnut (Pterocarya stenoptera): Insights from transcriptomics. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115307. [PMID: 37499386 DOI: 10.1016/j.ecoenv.2023.115307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/21/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Urban garden plants are frequently affected by drought, which can hinder their growth, development, and greening effect. Previous studies have indicated that Chinese wingnut (Pterocarya stenoptera) responds to drought stress by increasing the expression of thiamine synthesis genes. In this study, it was found that exogenous thiamine can effectively alleviate the negative effects of drought stress on plants. Forward transcriptome sequencing and physiological tests were further conducted to reveal the molecular mechanism of thiamine in alleviating drought stress. Results showed that exogenous thiamine activated the expression of eight chlorophyll synthesis genes in Chinese wingnut under drought stress. Moreover, physiological indicators proved that chlorophyll content increased in leaves of Chinese wingnut with thiamine treatment under drought stress. Photosynthesis genes were also activated in Chinese wingnut treated with exogenous thiamine under drought stress, as supported by photosynthetic indicators PIabs and PItotal. Additionally, exogenous thiamine stimulated the expression of genes in the auxin-activated signaling pathway, thus attenuating the effects of drought stress. This study demonstrates the molecular mechanism of thiamine in mitigating the effects of drought stress on non-model woody plants lacking transgenic systems. This study also provides an effective method to mitigate the negative impacts of drought stress on plants.
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Affiliation(s)
- Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Shu-Chen Wang
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Yong Li
- College of Life Science and Technology, Inner Mongolia Normal University, Huhehaote, China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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Pigoni M, Uzquiano A, Paulsen B, Kedaigle AJ, Yang SM, Symvoulidis P, Adiconis X, Velasco S, Sartore R, Kim K, Tucewicz A, Tropp SY, Tsafou K, Jin X, Barrett L, Chen F, Boyden ES, Regev A, Levin JZ, Arlotta P. Cell-type specific defects in PTEN-mutant cortical organoids converge on abnormal circuit activity. Hum Mol Genet 2023; 32:2773-2786. [PMID: 37384417 PMCID: PMC10481103 DOI: 10.1093/hmg/ddad107] [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: 03/31/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023] Open
Abstract
De novo heterozygous loss-of-function mutations in phosphatase and tensin homolog (PTEN) are strongly associated with autism spectrum disorders; however, it is unclear how heterozygous mutations in this gene affect different cell types during human brain development and how these effects vary across individuals. Here, we used human cortical organoids from different donors to identify cell-type specific developmental events that are affected by heterozygous mutations in PTEN. We profiled individual organoids by single-cell RNA-seq, proteomics and spatial transcriptomics and revealed abnormalities in developmental timing in human outer radial glia progenitors and deep-layer cortical projection neurons, which varied with the donor genetic background. Calcium imaging in intact organoids showed that both accelerated and delayed neuronal development phenotypes resulted in similar abnormal activity of local circuits, irrespective of genetic background. The work reveals donor-dependent, cell-type specific developmental phenotypes of PTEN heterozygosity that later converge on disrupted neuronal activity.
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Affiliation(s)
- Martina Pigoni
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ana Uzquiano
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bruna Paulsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amanda J Kedaigle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sung Min Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Panagiotis Symvoulidis
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Silvia Velasco
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rafaela Sartore
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashley Tucewicz
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Yoshimi Tropp
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kalliopi Tsafou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Lindy Barrett
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fei Chen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Edward S Boyden
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Harvard-MIT Health Sciences & Technology Program (HST), Harvard Medical School, Boston, MA 02115, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA 02138, USA
- Department of Brain of Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Xiong L, Li Y, Yu H, Wei Y, Li H, Ji X. Whole genome analysis and cold adaptation strategies of Pseudomonas sivasensis W-6 isolated from the Napahai plateau wetland. Sci Rep 2023; 13:14190. [PMID: 37648730 PMCID: PMC10468529 DOI: 10.1038/s41598-023-41323-x] [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: 01/02/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Microbial communities of wetlands play key roles in the earth's ecology and stability. To elucidate the cold adaptation mechanisms of bacteria in plateau wetlands, we conducted comparative genomic analyses of Pseudomonas sivasensis and closely related lineages. The genome of P. sivasensis W-6, a cold-adapted bacterium isolated from the Napahai plateau wetland, was sequenced and analyzed. The genome length was 6,109,123 bp with a G+C content of 59.5%. Gene prediction yielded 5360 protein-coding sequences, 70 tRNAs, 24 gene islands, and 2 CRISPR sequences. The isolate contained evidence of horizontal gene transfer events during its evolution. Two prophages were predicted and indicated that W-6 was a lysogen. The cold adaptation of the W-6 strain showed psychrophilic rather than psychrotrophic characteristics. Cold-adapted bacterium W-6 can utilize glycogen and trehalose as resources, associated with carbohydrate-active enzymes, and survive in a low-temperature environment. In addition, the cold-adapted mechanisms of the W-6 included membrane fluidity by changing the unsaturated fatty acid profile, the two-component regulatory systems, anti-sense transcription, the role played by rpsU genes in the translation process, etc. The genome-wide analysis of W-6 provided a deeper understanding of cold-adapted strategies of bacteria in environments. We elucidated the adaptive mechanism of the psychrophilic W-6 strain for survival in a cold environment, which provided a basis for further study on host-phage coevolution.
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Affiliation(s)
- Lingling Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yanmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hang Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
| | - Xiuling Ji
- Medical School, Kunming University of Science and Technology, Kunming, China.
- Yunnan International Joint Laboratory of Research and Development of Crop Safety Production on Heavy Metal Pollution Areas, Kunming, China.
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Seo JJ, Jung SJ, Yang J, Choi DE, Kim VN. Functional viromic screens uncover regulatory RNA elements. Cell 2023:S0092-8674(23)00675-X. [PMID: 37413987 DOI: 10.1016/j.cell.2023.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/21/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023]
Abstract
The number of sequenced viral genomes has surged recently, presenting an opportunity to understand viral diversity and uncover unknown regulatory mechanisms. Here, we conducted a screening of 30,367 viral segments from 143 species representing 96 genera and 37 families. Using a library of viral segments in 3' UTR, we identified hundreds of elements impacting RNA abundance, translation, and nucleocytoplasmic distribution. To illustrate the power of this approach, we investigated K5, an element conserved in kobuviruses, and found its potent ability to enhance mRNA stability and translation in various contexts, including adeno-associated viral vectors and synthetic mRNAs. Moreover, we identified a previously uncharacterized protein, ZCCHC2, as a critical host factor for K5. ZCCHC2 recruits the terminal nucleotidyl transferase TENT4 to elongate poly(A) tails with mixed sequences, delaying deadenylation. This study provides a unique resource for virus and RNA research and highlights the potential of the virosphere for biological discoveries.
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Affiliation(s)
- Jenny J Seo
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo-Jin Jung
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Da-Eun Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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40
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Mou CY, Li Q, Huang ZP, Ke HY, Zhao H, Zhao ZM, Duan YL, Li HD, Xiao Y, Qian ZM, Du J, Zhou J, Zhang L. PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense. BMC Genomics 2023; 24:340. [PMID: 37340366 DOI: 10.1186/s12864-023-09442-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/11/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn. RESULTS A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified. CONCLUSIONS In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.
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Affiliation(s)
- Cheng-Yan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhi-Peng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hong-Yu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhong-Meng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yuan-Liang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hua-Dong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yu Xiao
- Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Zhou-Ming Qian
- Chengdu Eaters Agricultural Group Co., Ltd, Chengdu, Sichuan, 610000, China
| | - Jun Du
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
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Zhang Z, Xia T, Zhou S, Yang X, Lyu T, Wang L, Fang J, Wang Q, Dou H, Zhang H. High-Quality Chromosome-Level Genome Assembly of the Corsac Fox ( Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments. Int J Mol Sci 2023; 24:ijms24119599. [PMID: 37298549 DOI: 10.3390/ijms24119599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.
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Affiliation(s)
- Zhihao Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tianshu Lyu
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
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Wang X, Huang X, Chen L, Xie Z, Tan S, Qin X, Chen T, Huang Y, Xi J, Chen H, Yi K. Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave. PLANTS (BASEL, SWITZERLAND) 2023; 12:2020. [PMID: 37653937 PMCID: PMC10222593 DOI: 10.3390/plants12102020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/06/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Agave species are widely planted for fiber production. However, the molecular basis of agave fiber development has not been well understood. In this study, we performed a transcriptomic analysis in A. amaniensi, a well-known variety with high-quality fiber production. Approximately 43.87 million clean reads were obtained using Illumina sequencing. The de novo assembly produced 66,746 unigrams, 54% of which were annotated in a public database. In the Nr database, 21,490 unigenes of A. amaniensis were shown to be most closely related to Asparagus officinalis. Nine expansin A orthologs with full coding regions were obtained, which were named EXP1a, EXP1b, EXP2, EXP3, EXP4a, EXP4b, EXP11, EXP12, and EXP13. The maximum likelihood phylogenetic tree revealed the species-specific expansion of expansin genes in Arabidopsis, rice and agave. The expression analysis suggested the negative correlation between the expression of expansin genes and the leaf growth rate, except AhEXP11. Moreover, expansin genes were differentially affected by abiotic and biotic stresses. Notably, AhEXP2 expression level was highly upgraded after the infection of Phytophthora nicotiana. Nutrient deficiency also influent expansin genes expression. Together, our research will benefit future studies related to fiber development, disease resistance and nutrient usage in agave.
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Affiliation(s)
- Xuxia Wang
- Urban Construction College, Wuchang Shouyi University, Wuhan 430064, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Lisha Chen
- Quality Supervision, Inspection and Testing Center of Sisal and Products, Ministry of Agriculture and Rural Affairs, Zhanjiang 524022, China
| | - Zhouli Xie
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Yanlei Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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Kashif M, Sang Y, Mo S, Rehman SU, Khan S, Khan MR, He S, Jiang C. Deciphering the biodesulfurization pathway employing marine mangrove Bacillus aryabhattai strain NM1-A2 according to whole genome sequencing and transcriptome analyses. Genomics 2023; 115:110635. [PMID: 37150229 DOI: 10.1016/j.ygeno.2023.110635] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/22/2023] [Accepted: 05/03/2023] [Indexed: 05/09/2023]
Abstract
In the biogeochemical cycle, sulfur oxidation plays a vital role and is typically referred to as the elemental sulfur or reductive sulfide oxidation process. This study aimed to characterize a subtropical mangrove-isolated bacterial strain using biochemical, whole-genome, and transcriptome sequencing analyses to enhance our understanding of sulfur metabolism and biodegradation from a molecular genetic perspective. Strain NM1-A2 was characterized as Gram-positive and found to have a close molecular phylogenetic relationship with Bacillus aryabhattai. NM1-A2 efficiently converted dibenzothiophene (DBT) into 2-hydroxybiphenyl (2-HBP) via a 4S pathway with 95% efficiency, using enzymes encoded by the dsz operon (dszA, dszB, and dszC), which determine monooxygenases (DszA & DszC) and desulfinase (DszB). The whole-genome sequence of NM1-A2 had a length of approximately 5,257,678 bp and included 16 sulfur metabolism-related genes, featuring the ABC transport system, small subunit (ssu) and cysteine (cys) gene families, and adenosine 5'-phosphosulfate (APS) and 3'-phosphoadenosine-5'-phosphosulfate (PAPS) biosynthesis-related genes. Transcriptomic analysis of NM1-A2 using three sulfur groups-magnesium sulfate (MS), sulfur powder (SP), and sodium thiosulfate (ST) resulted in a significant number of differentially expressed genes (1200, 2304, and 2001, respectively). This analysis revealed that intracellular cysteine concentration directly regulated the expression of cys and ssu genes. Sulfate did not directly affect cys gene expression but repressed ssu gene expression. The cys gene expression levels decreased during the conversion of sulfate to sulfide and cysteine. The transcriptomic data was validated by analyzing the expression patterns of NM1-A2 using real-time quantitative PCR validation analysis. The expression levels of cysl, mccB, and nrnA were significantly upregulated, while cysH, metB, and sat were downregulated in the SP, ST, and MS groups, respectively. This research contributes to our understanding of marine mangrove microorganisms' bacterial efficiency through characterization, whole-genome, and transcriptome sequencing-based molecular degradation of organic compounds in the mangrove ecosystem, which may enhance nutrient availability.
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Affiliation(s)
- Muhammad Kashif
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yimeng Sang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Shuming Mo
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Saif Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Sohail Khan
- College of Resources and Environment, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, China
| | - Muhammad Rafiullah Khan
- Department of Food Engineering, Pak-Austria Fachhochschule: Institute of Applied Sciences and Technology, Khanpur Road, Mang, Haripur, Pakistan
| | - Sheng He
- Guangxi Birth Defects Prevention and Control Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region. Nanning 530033, China
| | - Chengjian Jiang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning 530007, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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Zafar H, Saier MH. Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery. Cells 2023; 12:cells12091213. [PMID: 37174613 PMCID: PMC10177376 DOI: 10.3390/cells12091213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) first emerged in 2019 in China and has resulted in millions of human morbidities and mortalities across the globe. Evidence has been provided that this novel virus originated in animals, mutated, and made the cross-species jump to humans. At the time of this communication, the Coronavirus disease (COVID-19) may be on its way to an endemic form; however, the threat of the virus is more for susceptible (older and immunocompromised) people. The human body has millions of bacterial cells that influence health and disease. As a consequence, the bacteriomes in the human body substantially influence human health and disease. The bacteriomes in the body and the immune system seem to be in constant association during bacterial and viral infections. In this review, we identify various bacterial spp. In major bacteriomes (oral, nasal, lung, and gut) of the body in healthy humans and compare them with dysbiotic bacteriomes of COVID-19 patients. We try to identify key bacterial spp. That have a positive effect on the functionality of the immune system and human health. These select bacterial spp. Could be used as potential probiotics to counter or prevent COVID-19 infections. In addition, we try to identify key metabolites produced by probiotic bacterial spp. That could have potential anti-viral effects against SARS-CoV-2. These metabolites could be subject to future therapeutic trials to determine their anti-viral efficacies.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA 92093-0116, USA
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Milton H Saier
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, CA 92093-0116, USA
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Wang T, Wang B, Hua X, Tang H, Zhang Z, Gao R, Qi Y, Zhang Q, Wang G, Yu Z, Huang Y, Zhang Z, Mei J, Wang Y, Zhang Y, Li Y, Meng X, Wang Y, Pan H, Chen S, Li Z, Shi H, Liu X, Deng Z, Chen B, Zhang M, Gu L, Wang J, Ming R, Yao W, Zhang J. A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus. NATURE PLANTS 2023; 9:554-571. [PMID: 36997685 DOI: 10.1038/s41477-023-01378-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.
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Affiliation(s)
- Tianyou Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baiyu Wang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xiuting Hua
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiting Gao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yiying Qi
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gang Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, China
| | - Zehuai Yu
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Yongji Huang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou, China
| | - Zhe Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Mei
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhao Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yixing Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yihan Li
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Xue Meng
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongjun Wang
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haoran Pan
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqi Chen
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Li
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihong Shi
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinlong Liu
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Baoshan Chen
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianping Wang
- Department of Agronomy, University of Florida, Gainesville, FL, USA
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
| | - Jisen Zhang
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, China.
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Nguyen R, Sokhansanj BA, Polikar R, Rosen GL. Complet+: a computationally scalable method to improve completeness of large-scale protein sequence clustering. PeerJ 2023; 11:e14779. [PMID: 36785708 PMCID: PMC9921987 DOI: 10.7717/peerj.14779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/03/2023] [Indexed: 02/10/2023] Open
Abstract
A major challenge for clustering algorithms is to balance the trade-off between homogeneity, i.e., the degree to which an individual cluster includes only related sequences, and completeness, the degree to which related sequences are broken up into multiple clusters. Most algorithms are conservative in grouping sequences with other sequences. Remote homologs may fail to be clustered together and instead form unnecessarily distinct clusters. The resulting clusters have high homogeneity but completeness that is too low. We propose Complet+, a computationally scalable post-processing method to increase the completeness of clusters without an undue cost in homogeneity. Complet+ proves to effectively merge closely-related clusters of protein that have verified structural relationships in the SCOPe classification scheme, improving the completeness of clustering results at little cost to homogeneity. Applying Complet+ to clusters obtained using MMseqs2's clusterupdate achieves an increased V-measure of 0.09 and 0.05 at the SCOPe superfamily and family levels, respectively. Complet+ also creates more biologically representative clusters, as shown by a substantial increase in Adjusted Mutual Information (AMI) and Adjusted Rand Index (ARI) metrics when comparing predicted clusters to biological classifications. Complet+ similarly improves clustering metrics when applied to other methods, such as CD-HIT and linclust. Finally, we show that Complet+ runtime scales linearly with respect to the number of clusters being post-processed on a COG dataset of over 3 million sequences. Code and supplementary information is available on Github: https://github.com/EESI/Complet-Plus.
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Affiliation(s)
- Rachel Nguyen
- Drexel University, Philadelphia, United States of America
| | | | - Robi Polikar
- Rowan University, Glassboro, NJ, United States of America
| | - Gail L. Rosen
- Drexel University, Philadelphia, United States of America
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Han X, Zhang Y, Zhang Q, Ma N, Liu X, Tao W, Lou Z, Zhong C, Deng XW, Li D, He H. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. MOLECULAR PLANT 2023; 16:452-470. [PMID: 36588343 DOI: 10.1016/j.molp.2022.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value, especially because of the high content of vitamin C in its fruit. In this study, we de novo assembled two telomere-to-telomere kiwifruit genomes from Actinidia chinensis var. 'Donghong' (DH) and Actinidia latifolia 'Kuoye' (KY), with total lengths of 608 327 852 and 640 561 626 bp for 29 chromosomes, respectively. With a burst of structural variants involving inversion, translocations, and duplications within 8.39 million years, the metabolite content of DH and KY exhibited differences in saccharides, lignans, and vitamins. A regulatory ERF098 transcription factor family has expanded in KY and Actinidia eriantha, both of which have ultra-high vitamin C content. With each assembly phased into two complete haplotypes, we identified allelic variations between two sets of haplotypes, leading to protein sequence variations in 26 494 and 27 773 gene loci and allele-specific expression of 4687 and 12 238 homozygous gene pairs. Synchronized metabolome and transcriptome changes during DH fruit development revealed the same dynamic patterns in expression levels and metabolite contents; free fatty acids and flavonols accumulated in the early stages, but sugar substances and amino acids accumulated in the late stages. The AcSWEET9b gene that exhibits allelic dominance was further identified to positively correlate with high sucrose content in fruit. Compared with wild varieties and other Actinidia species, AcSWEET9b promoters were selected in red-flesh kiwifruits that have increased fruit sucrose content, providing a possible explanation on why red-flesh kiwifruits are sweeter. Collectively, these two gap-free kiwifruit genomes provide a valuable genetic resource for investigating domestication mechanisms and genome-based breeding of kiwifruit.
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Affiliation(s)
- Xue Han
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yilin Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Ni Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoying Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Wenjing Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zhiying Lou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China.
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China.
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48
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Sheng K, Sun Y, Liu M, Cao Y, Han Y, Li C, Muhammad U, Daud MK, Wang W, Li H, Samrana S, Hui Y, Zhu S, Chen J, Zhao T. A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol. PLANT COMMUNICATIONS 2023; 4:100421. [PMID: 35949167 PMCID: PMC9860168 DOI: 10.1016/j.xplc.2022.100421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 05/31/2023]
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49
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Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese. Commun Biol 2022; 5:1191. [DOI: 10.1038/s42003-022-04125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractGeese are herbivorous birds that play an essential role in the agricultural economy. We construct the chromosome-level genome of a Chinese indigenous goose (the Xingguo gray goose, XGG; Anser cygnoides) and analyze the adaptation of fat storage capacity in the goose liver during the evolution of Anatidae. Genomic resequencing of 994 geese is used to investigate the genetic relationships of geese, which supports the dual origin of geese (Anser cygnoides and Anser anser). Chinese indigenous geese show higher genetic diversity than European geese, and a scientific conservation program can be established to preserve genetic variation for each breed. We also find that a 14-bp insertion in endothelin receptor B subtype 2 (EDNRB2) that determines the white plumage of Chinese domestic geese is a natural mutation, and the linkaged alleles rapidly increase in frequency as a result of genetic hitchhiking, leading to the formation of completely different haplotypes of white geese under strong artificial selection. These genomic resources and our findings will facilitate marker-assisted breeding of geese and provide a foundation for further research on geese genetics and evolution.
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50
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Cui S, Gu Z, Wang W, Tang X, Zhang Q, Mao B, Zhang H, Zhao J. Characterization of peptides available to different bifidobacteria. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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