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Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species

Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three cl...

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Autores principales: Zheng, Zeyu, Li, Ying, Li, Minjie, Li, Guiting, Du, Xin, Hongyin, Hu, Yin, Mou, Lu, Zhiqiang, Zhang, Xu, Shrestha, Nawal, Liu, Jianquan, Yang, Yongzhi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902934/
https://www.ncbi.nlm.nih.gov/pubmed/33643339
http://dx.doi.org/10.3389/fpls.2021.581704
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author Zheng, Zeyu
Li, Ying
Li, Minjie
Li, Guiting
Du, Xin
Hongyin, Hu
Yin, Mou
Lu, Zhiqiang
Zhang, Xu
Shrestha, Nawal
Liu, Jianquan
Yang, Yongzhi
author_facet Zheng, Zeyu
Li, Ying
Li, Minjie
Li, Guiting
Du, Xin
Hongyin, Hu
Yin, Mou
Lu, Zhiqiang
Zhang, Xu
Shrestha, Nawal
Liu, Jianquan
Yang, Yongzhi
author_sort Zheng, Zeyu
collection PubMed
description Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.
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spelling pubmed-79029342021-02-25 Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species Zheng, Zeyu Li, Ying Li, Minjie Li, Guiting Du, Xin Hongyin, Hu Yin, Mou Lu, Zhiqiang Zhang, Xu Shrestha, Nawal Liu, Jianquan Yang, Yongzhi Front Plant Sci Plant Science Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research. Frontiers Media S.A. 2021-02-10 /pmc/articles/PMC7902934/ /pubmed/33643339 http://dx.doi.org/10.3389/fpls.2021.581704 Text en Copyright © 2021 Zheng, Li, Li, Li, Du, Hongyin, Yin, Lu, Zhang, Shrestha, Liu and Yang. http://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 Plant Science
Zheng, Zeyu
Li, Ying
Li, Minjie
Li, Guiting
Du, Xin
Hongyin, Hu
Yin, Mou
Lu, Zhiqiang
Zhang, Xu
Shrestha, Nawal
Liu, Jianquan
Yang, Yongzhi
Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species
title Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species
title_full Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species
title_fullStr Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species
title_full_unstemmed Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species
title_short Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species
title_sort whole-genome diversification analysis of the hornbeam species reveals speciation and adaptation among closely related species
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902934/
https://www.ncbi.nlm.nih.gov/pubmed/33643339
http://dx.doi.org/10.3389/fpls.2021.581704
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