Analysis of new retrogenes provides insight into dog adaptive evolution
Abstract The origin and subsequent evolution of new genes have been considered as an important source of genetic and phenotypic diversity in organisms. Dog breeds show great phenotypic diversity for morphological, physiological, and behavioral traits. However, the contributions of newly originated r...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2019-10-01
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| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.5620 |
| _version_ | 1818351597002948608 |
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| author | Xiang Gao Yan Li Adeyinka A. Adetula Yu Wu Hong Chen |
| author_facet | Xiang Gao Yan Li Adeyinka A. Adetula Yu Wu Hong Chen |
| author_sort | Xiang Gao |
| collection | DOAJ |
| description | Abstract The origin and subsequent evolution of new genes have been considered as an important source of genetic and phenotypic diversity in organisms. Dog breeds show great phenotypic diversity for morphological, physiological, and behavioral traits. However, the contributions of newly originated retrogenes, which provide important genetic bases for dog species differentiation and adaptive traits, are largely unknown. Here, we analyzed the dog genome to identify new RNA‐based duplications and comprehensively investigated their origin, evolution, functions in adaptive traits, and gene movement processes. First, we totally identified 3,025 retrocopies including 476 intact retrogenes, 2,518 retropseudogenes, and 31 chimerical retrogenes. Second, selective pressure along with ESTs expression analysis showed that most of the intact retrogenes were significantly under stronger purifying selection and subjected to more functional constraints when compared to retropseudogenes. Furthermore, a large number of retrocopies and chimerical retrogenes that occurred approximately 22 million years ago implied a burst of retrotransposition in the dog genome after the divergence time between dog and its closely related species red fox. Interestingly, GO and pathway analyses showed that new retrogenes had expanded in glutathione biosynthetic/metabolic process which likely provided important genetic basis for dogs' adaptation to scavenge human waste dumps. Finally, consistent with the results in human and mouse, a significant excess of functional retrogenes movement on and off the X chromosome in the dog confirmed a general pattern of gene movement process in mammals which was likely driven by natural selection or sexual antagonism. Together, these results increase our understanding that new retrogenes can reshape the dog genome and provide further exploration of the molecular mechanisms underlying the dogs' adaptive evolution. |
| first_indexed | 2024-12-13T18:40:16Z |
| format | Article |
| id | doaj.art-1a4f76c303d545d6961b5cff99cd433e |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-12-13T18:40:16Z |
| publishDate | 2019-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-1a4f76c303d545d6961b5cff99cd433e2022-12-21T23:35:14ZengWileyEcology and Evolution2045-77582019-10-01919111851119710.1002/ece3.5620Analysis of new retrogenes provides insight into dog adaptive evolutionXiang Gao0Yan Li1Adeyinka A. Adetula2Yu Wu3Hong Chen4Center Laboratory Renmin Hospital of Wuhan University Wuhan ChinaDepartment of Infectious Diseases Zhongnan Hospital of Wuhan University Wuhan ChinaKey Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction Huazhong Agricultural University Wuhan ChinaOilfield Community D-1-902 Wuhan ChinaDepartment of Scientific Research Renmin Hospital of Wuhan University Wuhan ChinaAbstract The origin and subsequent evolution of new genes have been considered as an important source of genetic and phenotypic diversity in organisms. Dog breeds show great phenotypic diversity for morphological, physiological, and behavioral traits. However, the contributions of newly originated retrogenes, which provide important genetic bases for dog species differentiation and adaptive traits, are largely unknown. Here, we analyzed the dog genome to identify new RNA‐based duplications and comprehensively investigated their origin, evolution, functions in adaptive traits, and gene movement processes. First, we totally identified 3,025 retrocopies including 476 intact retrogenes, 2,518 retropseudogenes, and 31 chimerical retrogenes. Second, selective pressure along with ESTs expression analysis showed that most of the intact retrogenes were significantly under stronger purifying selection and subjected to more functional constraints when compared to retropseudogenes. Furthermore, a large number of retrocopies and chimerical retrogenes that occurred approximately 22 million years ago implied a burst of retrotransposition in the dog genome after the divergence time between dog and its closely related species red fox. Interestingly, GO and pathway analyses showed that new retrogenes had expanded in glutathione biosynthetic/metabolic process which likely provided important genetic basis for dogs' adaptation to scavenge human waste dumps. Finally, consistent with the results in human and mouse, a significant excess of functional retrogenes movement on and off the X chromosome in the dog confirmed a general pattern of gene movement process in mammals which was likely driven by natural selection or sexual antagonism. Together, these results increase our understanding that new retrogenes can reshape the dog genome and provide further exploration of the molecular mechanisms underlying the dogs' adaptive evolution.https://doi.org/10.1002/ece3.5620adaptive evolutiongene movementnew geneson and off the X chromosomeretrogene |
| spellingShingle | Xiang Gao Yan Li Adeyinka A. Adetula Yu Wu Hong Chen Analysis of new retrogenes provides insight into dog adaptive evolution Ecology and Evolution adaptive evolution gene movement new genes on and off the X chromosome retrogene |
| title | Analysis of new retrogenes provides insight into dog adaptive evolution |
| title_full | Analysis of new retrogenes provides insight into dog adaptive evolution |
| title_fullStr | Analysis of new retrogenes provides insight into dog adaptive evolution |
| title_full_unstemmed | Analysis of new retrogenes provides insight into dog adaptive evolution |
| title_short | Analysis of new retrogenes provides insight into dog adaptive evolution |
| title_sort | analysis of new retrogenes provides insight into dog adaptive evolution |
| topic | adaptive evolution gene movement new genes on and off the X chromosome retrogene |
| url | https://doi.org/10.1002/ece3.5620 |
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