First de novo whole genome sequencing and assembly of the bar-headed goose

NWIPB OpenIR

	First de novo whole genome sequencing and assembly of the bar-headed goose
	Wang, Wen; Wang, Fang; Hao, Rongkai; Wang, Aizhen; Sharshov, Kirill; Druzyaka, Alexey; Lancuo, Zhuoma; Shi, Yuetong; Feng, Shuo
	2020
发表期刊	PEERJ
卷号	8
摘要	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 barheaded 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 barheaded geese at the genomic level.
关键词	Bar-headed goose Anser indicus 10X Genomics Chromium Avian genomes Comparative genomics Conservation genomics High-altitude adaptation Positive selection Hypoxia Qinghai-Tibetan Plateau
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/60360
专题	中国科学院西北高原生物研究所
推荐引用方式 GB/T 7714	Wang, Wen,Wang, Fang,Hao, Rongkai,et al. First de novo whole genome sequencing and assembly of the bar-headed goose[J]. PEERJ,2020,8.
APA	Wang, Wen.,Wang, Fang.,Hao, Rongkai.,Wang, Aizhen.,Sharshov, Kirill.,...&Feng, Shuo.(2020).First de novo whole genome sequencing and assembly of the bar-headed goose.PEERJ,8.
MLA	Wang, Wen,et al."First de novo whole genome sequencing and assembly of the bar-headed goose".PEERJ 8(2020).