Comparative transcriptomics reveals the selection patterns of domesticated ramie
Abstract Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern...
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| Format: | Article |
| Language: | English |
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Wiley
2019-06-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.5271 |
| _version_ | 1818336806786039808 |
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| author | Kun‐Yong Huang Ai‐Guo Zhu Xiao‐Rong Chen Ya‐Liang Shi Qing Tang Xiao‐Fei Wang Zhi‐Min Sun Ming‐Bao Luan Jian‐Hua Chen |
| author_facet | Kun‐Yong Huang Ai‐Guo Zhu Xiao‐Rong Chen Ya‐Liang Shi Qing Tang Xiao‐Fei Wang Zhi‐Min Sun Ming‐Bao Luan Jian‐Hua Chen |
| author_sort | Kun‐Yong Huang |
| collection | DOAJ |
| description | Abstract Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern and genetic relationships among a cultivated variety of ramie (BNZ: B. nivea, ZZ1) and four wild species, BNT (B. nivea var. tenacissima), BNN (B. nivea var. nipononivea), BNW (B. nivea var. nivea), and BAN (B. nivea var. viridula), in the section Tilocnide, we performed an RNA sequencing analysis of these ramie species. The de novo assembly of the “all‐ramie” transcriptome yielded 119,114 unigenes with an average length of 633 bp, and a total of 7,084 orthologous gene pairs were identified. The phylogenetic tree showed that the cultivar BNZ clustered with BAN in one group, BNW was closely related to BNT, and BNN formed a separate group. Introgression analysis indicated that gene flow occurred from BNZ to BNN and BAN, and between BAN and BNN. Among these orthologs, 2,425 and 269 genes underwent significant purifying and positive selection, respectively. For these positively selected genes, oxidation–reduction process (GO:0055114) and stress response pathways (GO:0006950) were enriched, indicating that modulation of the cellular redox status was important during both ramie fiber evolution and improvement. Two genes related to the suppression of flowering and one gene annotated as a flowering‐promoting factor were subjected to positive selection, probably caused by human manipulation. Additionally, five genes were homologs of those involved in abiotic stress tolerance and disease resistance, with higher expression levels in the cultivar BNZ than in the wild species. Collectively, the results of this study indicated that domestication has resulted in the upregulation of many genes involved in the abiotic and biotic stress responses, fiber yield, and plant growth of ramie. |
| first_indexed | 2024-12-13T14:45:11Z |
| format | Article |
| id | doaj.art-fc3987f5cdf6442e832d10aa3c31225b |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-12-13T14:45:11Z |
| publishDate | 2019-06-01 |
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| series | Ecology and Evolution |
| spelling | doaj.art-fc3987f5cdf6442e832d10aa3c31225b2022-12-21T23:41:29ZengWileyEcology and Evolution2045-77582019-06-019127057706810.1002/ece3.5271Comparative transcriptomics reveals the selection patterns of domesticated ramieKun‐Yong Huang0Ai‐Guo Zhu1Xiao‐Rong Chen2Ya‐Liang Shi3Qing Tang4Xiao‐Fei Wang5Zhi‐Min Sun6Ming‐Bao Luan7Jian‐Hua Chen8Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaInstitute of Bast Fiber Crops in Jiangxi Yichun ChinaInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaInstitute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences/Key Laboratory of Stem‐Fiber Biomass and Engineering Microbiology Ministry of Agriculture Changsha ChinaAbstract Although domestication has dramatically altered the phenotype, physiology, and life history of ramie (Boehmeria nivea) plants, few studies have investigated the effects of domestication on the structure and expression pattern of genes in this fiber crop. To investigate the selective pattern and genetic relationships among a cultivated variety of ramie (BNZ: B. nivea, ZZ1) and four wild species, BNT (B. nivea var. tenacissima), BNN (B. nivea var. nipononivea), BNW (B. nivea var. nivea), and BAN (B. nivea var. viridula), in the section Tilocnide, we performed an RNA sequencing analysis of these ramie species. The de novo assembly of the “all‐ramie” transcriptome yielded 119,114 unigenes with an average length of 633 bp, and a total of 7,084 orthologous gene pairs were identified. The phylogenetic tree showed that the cultivar BNZ clustered with BAN in one group, BNW was closely related to BNT, and BNN formed a separate group. Introgression analysis indicated that gene flow occurred from BNZ to BNN and BAN, and between BAN and BNN. Among these orthologs, 2,425 and 269 genes underwent significant purifying and positive selection, respectively. For these positively selected genes, oxidation–reduction process (GO:0055114) and stress response pathways (GO:0006950) were enriched, indicating that modulation of the cellular redox status was important during both ramie fiber evolution and improvement. Two genes related to the suppression of flowering and one gene annotated as a flowering‐promoting factor were subjected to positive selection, probably caused by human manipulation. Additionally, five genes were homologs of those involved in abiotic stress tolerance and disease resistance, with higher expression levels in the cultivar BNZ than in the wild species. Collectively, the results of this study indicated that domestication has resulted in the upregulation of many genes involved in the abiotic and biotic stress responses, fiber yield, and plant growth of ramie.https://doi.org/10.1002/ece3.5271differentially expressed genesdomesticationKa/Ksphylogenetic relationshipramieselective pattern |
| spellingShingle | Kun‐Yong Huang Ai‐Guo Zhu Xiao‐Rong Chen Ya‐Liang Shi Qing Tang Xiao‐Fei Wang Zhi‐Min Sun Ming‐Bao Luan Jian‐Hua Chen Comparative transcriptomics reveals the selection patterns of domesticated ramie Ecology and Evolution differentially expressed genes domestication Ka/Ks phylogenetic relationship ramie selective pattern |
| title | Comparative transcriptomics reveals the selection patterns of domesticated ramie |
| title_full | Comparative transcriptomics reveals the selection patterns of domesticated ramie |
| title_fullStr | Comparative transcriptomics reveals the selection patterns of domesticated ramie |
| title_full_unstemmed | Comparative transcriptomics reveals the selection patterns of domesticated ramie |
| title_short | Comparative transcriptomics reveals the selection patterns of domesticated ramie |
| title_sort | comparative transcriptomics reveals the selection patterns of domesticated ramie |
| topic | differentially expressed genes domestication Ka/Ks phylogenetic relationship ramie selective pattern |
| url | https://doi.org/10.1002/ece3.5271 |
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