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

PeerJ

article

Wen Wang¹  Fang Wang²  Rongkai Hao³  Aizhen Wang⁴  Kirill Sharshov⁵  Alexey Druzyaka⁶  Zhuoma Lancuo⁷  Yuetong Shi⁸  Shuo Feng¹ 

[1] State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University;Northwest Institute of Plateau Biology, Chinese Academy of Sciences;Novogene Bioinformatics Institute;College of Eco-Environmental Engineering, Qinghai University;Research Institute of Experimental and Clinical Medicine;Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences;School of Finance and Economics, Qinghai University;KunLun College of Qinghai University

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;   

DOI  :  10.7717/peerj.8914

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundThe 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.MethodsIn this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation.Results10X 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.ConclusionWe 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.

【 授权许可】

CC BY