First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens)
Abstract Background The Hainan Partridge (Arborophila ardens, Phasianidae, Galliformes) is an endemic species of Hainan Island, China, and it is classified as globally vulnerable species. There are at least 16 species in genus Arborophila and no genome sequence is available. Methods The whole genome...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2018-12-01
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| Series: | Avian Research |
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| Online Access: | http://link.springer.com/article/10.1186/s40657-018-0136-3 |
| _version_ | 1828075515211153408 |
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| author | Chuang Zhou Shuai Zheng Xue Jiang Wei Liang Megan Price Zhenxin Fan Yang Meng Bisong Yue |
| author_facet | Chuang Zhou Shuai Zheng Xue Jiang Wei Liang Megan Price Zhenxin Fan Yang Meng Bisong Yue |
| author_sort | Chuang Zhou |
| collection | DOAJ |
| description | Abstract Background The Hainan Partridge (Arborophila ardens, Phasianidae, Galliformes) is an endemic species of Hainan Island, China, and it is classified as globally vulnerable species. There are at least 16 species in genus Arborophila and no genome sequence is available. Methods The whole genome of Hainan Partridge was de novo sequenced (with shotgun approach on the Illumina 2000 platform) and assembled. Results The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus. About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected. A total of 17,376 protein-coding genes were predicted and their functions were annotated. The genome comparison between Hainan Partridge and Red Junglefowl (Gallus gallus) demonstrated a conserved genome structure. The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago (Mya). We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya, and then recovered to about 460,000 individuals. The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories, such as response to ultraviolet radiation were represented in GO distribution analysis. Conclusions We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution, adaption, conservation, not only on Hainan Partridge but also on Arborophila or Phasianidae species. |
| first_indexed | 2024-04-11T01:59:14Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2053-7166 |
| language | English |
| last_indexed | 2024-04-11T01:59:14Z |
| publishDate | 2018-12-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Avian Research |
| spelling | doaj.art-11ab8fc2ac9446db87fa37545ed704972023-01-03T04:19:04ZengKeAi Communications Co., Ltd.Avian Research2053-71662018-12-01911810.1186/s40657-018-0136-3First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens)Chuang Zhou0Shuai Zheng1Xue Jiang2Wei Liang3Megan Price4Zhenxin Fan5Yang Meng6Bisong Yue7Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan UniversityKey Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan UniversitySichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan UniversityMinistry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal UniversityKey Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan UniversitySichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan UniversityKey Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan UniversityKey Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan UniversityAbstract Background The Hainan Partridge (Arborophila ardens, Phasianidae, Galliformes) is an endemic species of Hainan Island, China, and it is classified as globally vulnerable species. There are at least 16 species in genus Arborophila and no genome sequence is available. Methods The whole genome of Hainan Partridge was de novo sequenced (with shotgun approach on the Illumina 2000 platform) and assembled. Results The genome size of Arborophila ardens is about 1.05 Gb with a high N50 scaffold length of 8.28 Mb and it is the first high quality genome announced in Arborophila genus. About 9.19% of the genome was identified as repeat sequences and about 5.88 million heterozygous SNPs were detected. A total of 17,376 protein-coding genes were predicted and their functions were annotated. The genome comparison between Hainan Partridge and Red Junglefowl (Gallus gallus) demonstrated a conserved genome structure. The phylogenetic analysis indicated that the Hainan Partridge possessed a basal phylogenetic position in Phasianidae and it was most likely derived from a common ancestor approximately 36.8 million years ago (Mya). We found that the Hainan Partridge population had experienced bottleneck and its effective population decreased from about 1,040,000 individuals 1.5 Mya to about 200,000 individuals 0.2 Mya, and then recovered to about 460,000 individuals. The number of 1:1 orthologous genes that were predicted to have undergone positive selection in the Hainan Partridge was 504 and some environmental adaptation related categories, such as response to ultraviolet radiation were represented in GO distribution analysis. Conclusions We announced the first high quality genome in Arborophila genus and it will be a valuable genomic resource for the further studies such as evolution, adaption, conservation, not only on Hainan Partridge but also on Arborophila or Phasianidae species.http://link.springer.com/article/10.1186/s40657-018-0136-3Hainan PartridgeArborophila ardensComparative genomicsPositive selection |
| spellingShingle | Chuang Zhou Shuai Zheng Xue Jiang Wei Liang Megan Price Zhenxin Fan Yang Meng Bisong Yue First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens) Avian Research Hainan Partridge Arborophila ardens Comparative genomics Positive selection |
| title | First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens) |
| title_full | First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens) |
| title_fullStr | First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens) |
| title_full_unstemmed | First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens) |
| title_short | First complete genome sequence in Arborophila and comparative genomics reveals the evolutionary adaptation of Hainan Partridge (Arborophila ardens) |
| title_sort | first complete genome sequence in arborophila and comparative genomics reveals the evolutionary adaptation of hainan partridge arborophila ardens |
| topic | Hainan Partridge Arborophila ardens Comparative genomics Positive selection |
| url | http://link.springer.com/article/10.1186/s40657-018-0136-3 |
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