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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Frontiers Media S.A.
2021-02-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.581704/full |
| _version_ | 1819160726288203776 |
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| author | Zeyu Zheng Ying Li Minjie Li Guiting Li Xin Du Hu Hongyin Mou Yin Zhiqiang Lu Xu Zhang Nawal Shrestha Jianquan Liu Yongzhi Yang |
| author_facet | Zeyu Zheng Ying Li Minjie Li Guiting Li Xin Du Hu Hongyin Mou Yin Zhiqiang Lu Xu Zhang Nawal Shrestha Jianquan Liu Yongzhi Yang |
| author_sort | Zeyu Zheng |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-22T17:01:02Z |
| format | Article |
| id | doaj.art-145f7c71baad4a81bb69fc07e3c25866 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-22T17:01:02Z |
| publishDate | 2021-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-145f7c71baad4a81bb69fc07e3c258662022-12-21T18:19:20ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-02-011210.3389/fpls.2021.581704581704Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related SpeciesZeyu Zheng0Ying Li1Minjie Li2Guiting Li3Xin Du4Hu Hongyin5Mou Yin6Zhiqiang Lu7Xu Zhang8Nawal Shrestha9Jianquan Liu10Yongzhi Yang11State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaCAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaState Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, ChinaSpeciation 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.https://www.frontiersin.org/articles/10.3389/fpls.2021.581704/fullspeciationadaptationCarpinusdivergenceselectionCNV |
| spellingShingle | Zeyu Zheng Ying Li Minjie Li Guiting Li Xin Du Hu Hongyin Mou Yin Zhiqiang Lu Xu Zhang Nawal Shrestha Jianquan Liu Yongzhi Yang Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species Frontiers in Plant Science speciation adaptation Carpinus divergence selection CNV |
| 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 | speciation adaptation Carpinus divergence selection CNV |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.581704/full |
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