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Wang MM, Song N, Guo SB, Yin XM. A comprehensive sampling of mitogenomes shows the utility to infer phylogeny of termites (Blattodea: Termitoidae). J Insect Sci 2024; 24:7. [PMID: 38491951 PMCID: PMC10944015 DOI: 10.1093/jisesa/ieae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
The mitogenome sequence data have been widely used in inferring the phylogeny of insects. In this study, we determined the complete mitogenome for Macrotermes sp. (Termitidae, Macrotermitinae) using next-generation sequencing. Macrotermes sp. possesses a typical insect mitogenome, displaying an identical gene order and gene content to other existing termite mitogenomes. We present the first prediction of the secondary structure of ribosomal RNA genes in termites. The rRNA secondary structures of Macrotermes sp. exhibit similarities to closely related insects and also feature distinctive characteristics in their helical structures. Together with 321 published mitogenomes of termites as ingroups and 8 cockroach mitogenomes as outgroups, we compiled the most comprehensive mitogenome sequence matrix for Termitoidae to date. Phylogenetic analyses were conducted using datasets employing different data coding strategies and various inference methods. Robust relationships were recovered at the family or subfamily level, demonstrating the utility of comprehensive mitogenome sampling in resolving termite phylogenies. The results supported the monophyly of Termitoidae, and consistent relationships within this group were observed across different analyses. Mastotermitidae was consistently recovered as the sister group to all other termite families. The families Hodotermitidae, Stolotermitidae, and Archotermopsidae formed the second diverging clade, followed by the Kalotermitidae. The Neoisoptera was consistently supported with strong node support, with Stylotermitidae being sister to the remaining families. Rhinotermitidae was found to be non-monophyletic, and Serritermitidae nested within the basal clades of Rhinotermitidae and was sister to Psammotermitinae. Overall, our phylogenetic results are largely consistent with earlier mitogenome studies.
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Affiliation(s)
- Miao-Miao Wang
- Department of Entomology, Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Nan Song
- Department of Entomology, Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Shi-Bao Guo
- Department of Plant Protection, Xinyang Agriculture and Forestry University, Xinyang 464399, China
| | - Xin-Ming Yin
- Department of Entomology, Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
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Zong D, Liu H, Gan P, Ma S, Liang H, Yu J, Li P, Jiang T, Sahu SK, Yang Q, Zhang D, Li L, Qiu X, Shao W, Yang J, Li Y, Guang X, He C. Chromosomal-scale genomes of two Rosa species provide insights into genome evolution and ascorbate accumulation. Plant J 2024; 117:1264-1280. [PMID: 37964640 DOI: 10.1111/tpj.16543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/07/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Rosa roxburghii and Rosa sterilis, two species belonging to the Rosaceae family, are widespread in the southwest of China. These species have gained recognition for their remarkable abundance of ascorbate in their fresh fruits, making them an ideal vitamin C resource. In this study, we generated two high-quality chromosome-scale genome assemblies for R. roxburghii and R. sterilis, with genome sizes of 504 and 981.2 Mb, respectively. Notably, we present a haplotype-resolved, chromosome-scale assembly for diploid R. sterilis. Our results indicated that R. sterilis originated from the hybridization of R. roxburghii and R. longicuspis. Genome analysis revealed the absence of recent whole-genome duplications in both species and identified a series of duplicated genes that possibly contributing to the accumulation of flavonoids. We identified two genes in the ascorbate synthesis pathway, GGP and GalLDH, that show signs of positive selection, along with high expression levels of GDP-d-mannose 3', 5'-epimerase (GME) and GDP-l-galactose phosphorylase (GGP) during fruit development. Furthermore, through co-expression network analysis, we identified key hub genes (MYB5 and bZIP) that likely regulate genes in the ascorbate synthesis pathway, promoting ascorbate biosynthesis. Additionally, we observed the expansion of terpene synthase genes in these two species and tissue expression patterns, suggesting their involvement in terpenoid biosynthesis. Our research provides valuable insights into genome evolution and the molecular basis of the high concentration of ascorbate in these two Rosa species.
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Affiliation(s)
- Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Peihua Gan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Shaojie Ma
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Hongping Liang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jinde Yu
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Peilin Li
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Tao Jiang
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Qingqing Yang
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Deguo Zhang
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 20032, China
| | - Xu Qiu
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
| | - Wenwen Shao
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | | | - Yonghe Li
- Yunnan Agricultural University, Kunming, 650201, China
| | - Xuanmin Guang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Chengzhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
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Guo S, Chen J, Song N. Phylogenomic analysis of Syrphoidea (Diptera: Syrphidae, Pipunculidae) based on the expanded mitogenomic data. Arch Insect Biochem Physiol 2023; 114:1-13. [PMID: 36597178 DOI: 10.1002/arch.21998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 09/27/2023]
Abstract
The mitochondrial genome has become the most widely used genomic resource in resolving the insect phylogenetic relationships. In this study, we assess the interrelationships among the syrphid and pipunculid members of Syrphoidea using mitochondrial genome sequences of 152 taxa, 9 of which are newly reported and three are assembled from the existing transcriptome data. The Pipunculidae was found to be deeply nested members of Schizophora, which resulted in a nonmonophyletic Syrphoidea. In the monophyletic Syrphidae, unequivocal robust support was found for Microdontinae as the sister group of all other Syrphidae. The subfamily Eristalinae was nonmonophyletic. The Pipizinae was recovered as the sister group to the Syrphinae, albeit with strong support. As a whole, our results are concord with previously established hypotheses on Syrphoidea from the genome scale data. The mitochondrial genomes were successful in producing a robustly supported phylogenetic framework for the Syrphoidea.
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Affiliation(s)
- Shibao Guo
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Junhua Chen
- Department of Plant Protection, College of Agronomy,Xinyang Agriculture and Forestry University, Xinyang, Henan, China
| | - Nan Song
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan, China
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Li HZ, Wu H, Song KK, Zhao HH, Tang XY, Zhang XH, Wang D, Dong SL, Liu F, Wang J, Li ZC, Yang L, Xiang QZ. Transcriptome analysis revealed enrichment pathways and regulation of gene expression associated with somatic embryogenesis in Camellia sinensis. Sci Rep 2023; 13:15946. [PMID: 37743377 PMCID: PMC10518320 DOI: 10.1038/s41598-023-43355-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023] Open
Abstract
The high frequency, stable somatic embryo system of tea has still not been established due to the limitations of its own characteristics and therefore severely restricts the genetic research and breeding process of tea plants. In this study, the transcriptome was used to illustrate the mechanisms of gene expression regulation in the somatic embryogenesis of tea plants. The number of DEGs for the (IS intermediate stage)_PS (preliminary stage), ES (embryoid stage)_IS and ES_PS stages were 109, 2848 and 1697, respectively. The enrichment analysis showed that carbohydrate metabolic processes were considerably enriched at the ES_IS stage and performed a key role in somatic embryogenesis, while enhanced light capture in photosystem I could provide the material basis for carbohydrates. The pathway analysis showed that the enriched pathways in IS_PS process were far less than those in ES_IS or ES_PS, and the photosynthesis and photosynthetic antenna protein pathway of DEGs in ES_IS or ES_PS stage were notably enriched and up-regulated. The key photosynthesis and photosynthesis antenna protein pathways and the Lhcb1 gene were discovered in tea plants somatic embryogenesis. These results were of great significance to clarify the mechanism of somatic embryogenesis and the breeding research of tea plants.
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Affiliation(s)
- Hao-Zhen Li
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Hui Wu
- AgricultureIsLife, Gembloux Agro-Bio Tech, Liege University, 5030, Gembloux 2, Belgium
| | - Kang-Kang Song
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Hui-Hui Zhao
- Ri Zhao Cha Cang Tea Co. Ltd, Ri'zhao, 276800, China
| | - Xiao-Yan Tang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, He'fei, 230036, China
| | - Xiao-Hua Zhang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Di Wang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Shao-Lin Dong
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China
| | - Feng Liu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Jun Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhong-Cong Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai'an, 271018, China.
| | - Qin-Zeng Xiang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
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Li H, Song K, Zhang X, Wang D, Dong S, Liu Y, Yang L. Application of Multi-Perspectives in Tea Breeding and the Main Directions. Int J Mol Sci 2023; 24:12643. [PMID: 37628823 PMCID: PMC10454712 DOI: 10.3390/ijms241612643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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