Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fpls.2023.1114284 http://hdl.handle.net/11449/249745 |
Resumo: | As one of the world’s top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies. |
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Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea populationCamellia sinensisnucleotide diversityphylogenypopulation geneticsselective sweepSNPsteatranscriptomeAs one of the world’s top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization Xinyang Normal University, HenanCollege of Life Sciences Xinyang Normal University, HenanLaboratory of Systematic Evolution and Biogeography of Woody Plants School of Ecology and Nature Conservation Beijing Forestry UniversityInstitute of Forestry Science Xinyang Forestry Bureau, HenanCollege of Engineering and Technology Northeast Forestry UniversityCollege of Agriculture Guizhou UniversityDepartment of Agricultural Livestock and Environmental Biotechnology Sao Paulo State UniversityDepartment of Agricultural Livestock and Environmental Biotechnology Sao Paulo State UniversityXinyang Normal UniversityBeijing Forestry UniversityXinyang Forestry BureauNortheast Forestry UniversityGuizhou UniversityUniversidade Estadual Paulista (UNESP)Cheng, LinLi, MenggeWang, YachaoHan, QunweiHao, YanlinQiao, ZhenZhang, WeiQiu, LinGong, AndongZhang, ZhihanLi, TaoLuo, ShanshanTang, LinshuangLiu, DaliangYin, HaoLu, SongBalbuena, Tiago Santana [UNESP]Zhao, Yiyong2023-07-29T16:08:06Z2023-07-29T16:08:06Z2023-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fpls.2023.1114284Frontiers in Plant Science, v. 14.1664-462Xhttp://hdl.handle.net/11449/24974510.3389/fpls.2023.11142842-s2.0-85149686488Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Plant Scienceinfo:eu-repo/semantics/openAccess2024-06-07T15:31:47Zoai:repositorio.unesp.br:11449/249745Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:25:46.254681Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population |
title |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population |
spellingShingle |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population Cheng, Lin Camellia sinensis nucleotide diversity phylogeny population genetics selective sweep SNPs tea transcriptome |
title_short |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population |
title_full |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population |
title_fullStr |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population |
title_full_unstemmed |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population |
title_sort |
Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population |
author |
Cheng, Lin |
author_facet |
Cheng, Lin Li, Mengge Wang, Yachao Han, Qunwei Hao, Yanlin Qiao, Zhen Zhang, Wei Qiu, Lin Gong, Andong Zhang, Zhihan Li, Tao Luo, Shanshan Tang, Linshuang Liu, Daliang Yin, Hao Lu, Song Balbuena, Tiago Santana [UNESP] Zhao, Yiyong |
author_role |
author |
author2 |
Li, Mengge Wang, Yachao Han, Qunwei Hao, Yanlin Qiao, Zhen Zhang, Wei Qiu, Lin Gong, Andong Zhang, Zhihan Li, Tao Luo, Shanshan Tang, Linshuang Liu, Daliang Yin, Hao Lu, Song Balbuena, Tiago Santana [UNESP] Zhao, Yiyong |
author2_role |
author author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Xinyang Normal University Beijing Forestry University Xinyang Forestry Bureau Northeast Forestry University Guizhou University Universidade Estadual Paulista (UNESP) |
dc.contributor.author.fl_str_mv |
Cheng, Lin Li, Mengge Wang, Yachao Han, Qunwei Hao, Yanlin Qiao, Zhen Zhang, Wei Qiu, Lin Gong, Andong Zhang, Zhihan Li, Tao Luo, Shanshan Tang, Linshuang Liu, Daliang Yin, Hao Lu, Song Balbuena, Tiago Santana [UNESP] Zhao, Yiyong |
dc.subject.por.fl_str_mv |
Camellia sinensis nucleotide diversity phylogeny population genetics selective sweep SNPs tea transcriptome |
topic |
Camellia sinensis nucleotide diversity phylogeny population genetics selective sweep SNPs tea transcriptome |
description |
As one of the world’s top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-07-29T16:08:06Z 2023-07-29T16:08:06Z 2023-01-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.3389/fpls.2023.1114284 Frontiers in Plant Science, v. 14. 1664-462X http://hdl.handle.net/11449/249745 10.3389/fpls.2023.1114284 2-s2.0-85149686488 |
url |
http://dx.doi.org/10.3389/fpls.2023.1114284 http://hdl.handle.net/11449/249745 |
identifier_str_mv |
Frontiers in Plant Science, v. 14. 1664-462X 10.3389/fpls.2023.1114284 2-s2.0-85149686488 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in Plant Science |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1808128809129476096 |