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Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae

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 ev...

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Autores principales: Cheng, Lin, Han, Qunwei, Chen, Fei, Li, Mengge, Balbuena, Tiago Santana, Zhao, Yiyong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9670182/
https://www.ncbi.nlm.nih.gov/pubmed/36406110
http://dx.doi.org/10.3389/fgene.2022.1031705
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author Cheng, Lin
Han, Qunwei
Chen, Fei
Li, Mengge
Balbuena, Tiago Santana
Zhao, Yiyong
author_facet Cheng, Lin
Han, Qunwei
Chen, Fei
Li, Mengge
Balbuena, Tiago Santana
Zhao, Yiyong
author_sort Cheng, Lin
collection PubMed
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.
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spelling pubmed-96701822022-11-18 Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae Cheng, Lin Han, Qunwei Chen, Fei Li, Mengge Balbuena, Tiago Santana Zhao, Yiyong Front Genet Genetics 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. Frontiers Media S.A. 2022-11-03 /pmc/articles/PMC9670182/ /pubmed/36406110 http://dx.doi.org/10.3389/fgene.2022.1031705 Text en Copyright © 2022 Cheng, Han, Chen, Li, Balbuena and Zhao. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Cheng, Lin
Han, Qunwei
Chen, Fei
Li, Mengge
Balbuena, Tiago Santana
Zhao, Yiyong
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
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_short 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
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9670182/
https://www.ncbi.nlm.nih.gov/pubmed/36406110
http://dx.doi.org/10.3389/fgene.2022.1031705
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