First de novo whole genome sequencing and assembly of the bar-headed goose
Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, bio...
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PeerJ Inc.
2020-04-01
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| Sarrera elektronikoa: | https://peerj.com/articles/8914.pdf |
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| author | Wen Wang Fang Wang Rongkai Hao Aizhen Wang Kirill Sharshov Alexey Druzyaka Zhuoma Lancuo Yuetong Shi Shuo Feng |
| author_facet | Wen Wang Fang Wang Rongkai Hao Aizhen Wang Kirill Sharshov Alexey Druzyaka Zhuoma Lancuo Yuetong Shi Shuo Feng |
| author_sort | Wen Wang |
| collection | DOAJ |
| description | Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level. |
| first_indexed | 2024-03-09T07:01:49Z |
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| spelling | doaj.art-0a3497d69ef748148a3dd63211ea7b112023-12-03T09:48:18ZengPeerJ Inc.PeerJ2167-83592020-04-018e891410.7717/peerj.8914First de novo whole genome sequencing and assembly of the bar-headed gooseWen Wang0Fang Wang1Rongkai Hao2Aizhen Wang3Kirill Sharshov4Alexey Druzyaka5Zhuoma Lancuo6Yuetong Shi7Shuo Feng8State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi’ning, Qinghai, ChinaNorthwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi’ning, Qinghai, ChinaNovogene Bioinformatics Institute, Beijing, ChinaCollege of Eco-Environmental Engineering, Qinghai University, Xi’ning, Qinghai, ChinaResearch Institute of Experimental and Clinical Medicine, Novosibirsk, RussiaInstitute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaSchool of Finance and Economics, Qinghai University, Xi’ning, Qinghai, ChinaKunLun College of Qinghai University, Xi’ning, Qinghai, ChinaState Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi’ning, Qinghai, ChinaBackground The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.https://peerj.com/articles/8914.pdfBar-headed gooseAnser indicus10X Genomics ChromiumAvian genomesComparative genomicsConservation genomics |
| spellingShingle | Wen Wang Fang Wang Rongkai Hao Aizhen Wang Kirill Sharshov Alexey Druzyaka Zhuoma Lancuo Yuetong Shi Shuo Feng First de novo whole genome sequencing and assembly of the bar-headed goose PeerJ Bar-headed goose Anser indicus 10X Genomics Chromium Avian genomes Comparative genomics Conservation genomics |
| title | First de novo whole genome sequencing and assembly of the bar-headed goose |
| title_full | First de novo whole genome sequencing and assembly of the bar-headed goose |
| title_fullStr | First de novo whole genome sequencing and assembly of the bar-headed goose |
| title_full_unstemmed | First de novo whole genome sequencing and assembly of the bar-headed goose |
| title_short | First de novo whole genome sequencing and assembly of the bar-headed goose |
| title_sort | first de novo whole genome sequencing and assembly of the bar headed goose |
| topic | Bar-headed goose Anser indicus 10X Genomics Chromium Avian genomes Comparative genomics Conservation genomics |
| url | https://peerj.com/articles/8914.pdf |
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