Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fgene.2022.1031705 http://hdl.handle.net/11449/249393 |
Resumo: | Hybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited. We proposed the conception and method of identifying allopolyploidy events by phylogenomics. The reconciliation and summary of nuclear multi-labeled gene family trees were adopted to untangle hybridization events from next-generation data in our novel phylogenomic approach. Given horticulturalists’ relatively clear cultivated crossbreeding history, the water lily family is a suitable case for examining recent allopolyploidy events. Here, we reconstructed and confirmed the well-resolved nuclear phylogeny for the Nymphaeales family in the context of geological time as a framework for identifying hybridization signals. We successfully identified two possible allopolyploidy events with the parental lineages for the hybrids in the family Nymphaeaceae based on summarization from multi-labeled gene family trees of Nymphaeales. The lineages where species Nymphaea colorata and Nymphaea caerulea are located may be the progenitors of horticultural cultivated species Nymphaea ‘midnight’ and Nymphaea ‘Woods blue goddess’. The proposed hybridization hypothesis is also supported by horticultural breeding records. Our methodology can be widely applied to identify hybridization events and theoretically facilitate the genome breeding design of hybrid plants. |
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Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceaeallopolyploidhybridizationmulti-labeled gene family treeNymphaeaceaephylogenomicsphylogenywater lilyHybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited. We proposed the conception and method of identifying allopolyploidy events by phylogenomics. The reconciliation and summary of nuclear multi-labeled gene family trees were adopted to untangle hybridization events from next-generation data in our novel phylogenomic approach. Given horticulturalists’ relatively clear cultivated crossbreeding history, the water lily family is a suitable case for examining recent allopolyploidy events. Here, we reconstructed and confirmed the well-resolved nuclear phylogeny for the Nymphaeales family in the context of geological time as a framework for identifying hybridization signals. We successfully identified two possible allopolyploidy events with the parental lineages for the hybrids in the family Nymphaeaceae based on summarization from multi-labeled gene family trees of Nymphaeales. The lineages where species Nymphaea colorata and Nymphaea caerulea are located may be the progenitors of horticultural cultivated species Nymphaea ‘midnight’ and Nymphaea ‘Woods blue goddess’. The proposed hybridization hypothesis is also supported by horticultural breeding records. Our methodology can be widely applied to identify hybridization events and theoretically facilitate the genome breeding design of hybrid plants.Henan International Joint Laboratory of Tea-oil Tree Biology and High-Value Utilization Xinyang Normal University, HenanCollege of Tropical Crops Hainan UniversityDepartment of Agricultural Livestock and Environmental Biotechnology UNESP, São PauloState Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development School of Life Sciences Fudan UniversityCollege of Agriculture Guizhou UniversityDepartment of Agricultural Livestock and Environmental Biotechnology UNESP, São PauloXinyang Normal UniversityHainan UniversityUniversidade Estadual Paulista (UNESP)Fudan UniversityGuizhou UniversityCheng, LinHan, QunweiChen, FeiLi, MenggeBalbuena, Tiago Santana [UNESP]Zhao, Yiyong2023-07-29T15:14:49Z2023-07-29T15:14:49Z2022-11-03info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fgene.2022.1031705Frontiers in Genetics, v. 13.1664-8021http://hdl.handle.net/11449/24939310.3389/fgene.2022.10317052-s2.0-85142340531Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers in Geneticsinfo:eu-repo/semantics/openAccess2024-06-07T15:31:20Zoai:repositorio.unesp.br:11449/249393Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:42:40.200653Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae |
title |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae |
spellingShingle |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae Cheng, Lin allopolyploid hybridization multi-labeled gene family tree Nymphaeaceae phylogenomics phylogeny water lily |
title_short |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae |
title_full |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae |
title_fullStr |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae |
title_full_unstemmed |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae |
title_sort |
Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae |
author |
Cheng, Lin |
author_facet |
Cheng, Lin Han, Qunwei Chen, Fei Li, Mengge Balbuena, Tiago Santana [UNESP] Zhao, Yiyong |
author_role |
author |
author2 |
Han, Qunwei Chen, Fei Li, Mengge Balbuena, Tiago Santana [UNESP] Zhao, Yiyong |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Xinyang Normal University Hainan University Universidade Estadual Paulista (UNESP) Fudan University Guizhou University |
dc.contributor.author.fl_str_mv |
Cheng, Lin Han, Qunwei Chen, Fei Li, Mengge Balbuena, Tiago Santana [UNESP] Zhao, Yiyong |
dc.subject.por.fl_str_mv |
allopolyploid hybridization multi-labeled gene family tree Nymphaeaceae phylogenomics phylogeny water lily |
topic |
allopolyploid hybridization multi-labeled gene family tree Nymphaeaceae phylogenomics phylogeny water lily |
description |
Hybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited. We proposed the conception and method of identifying allopolyploidy events by phylogenomics. The reconciliation and summary of nuclear multi-labeled gene family trees were adopted to untangle hybridization events from next-generation data in our novel phylogenomic approach. Given horticulturalists’ relatively clear cultivated crossbreeding history, the water lily family is a suitable case for examining recent allopolyploidy events. Here, we reconstructed and confirmed the well-resolved nuclear phylogeny for the Nymphaeales family in the context of geological time as a framework for identifying hybridization signals. We successfully identified two possible allopolyploidy events with the parental lineages for the hybrids in the family Nymphaeaceae based on summarization from multi-labeled gene family trees of Nymphaeales. The lineages where species Nymphaea colorata and Nymphaea caerulea are located may be the progenitors of horticultural cultivated species Nymphaea ‘midnight’ and Nymphaea ‘Woods blue goddess’. The proposed hybridization hypothesis is also supported by horticultural breeding records. Our methodology can be widely applied to identify hybridization events and theoretically facilitate the genome breeding design of hybrid plants. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-11-03 2023-07-29T15:14:49Z 2023-07-29T15:14:49Z |
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/fgene.2022.1031705 Frontiers in Genetics, v. 13. 1664-8021 http://hdl.handle.net/11449/249393 10.3389/fgene.2022.1031705 2-s2.0-85142340531 |
url |
http://dx.doi.org/10.3389/fgene.2022.1031705 http://hdl.handle.net/11449/249393 |
identifier_str_mv |
Frontiers in Genetics, v. 13. 1664-8021 10.3389/fgene.2022.1031705 2-s2.0-85142340531 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers in Genetics |
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 |
|
_version_ |
1808128407922278400 |