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

• Published in: PeerJ (San Francisco, CA) Vol. 8; p. e8914
• Main Authors: Wang, Wen, Wang, Fang, Hao, Rongkai, Wang, Aizhen, Sharshov, Kirill, Druzyaka, Alexey, Lancuo, Zhuoma, Shi, Yuetong, Feng, Shuo
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 06-04-2020; PeerJ, Inc; PeerJ Inc
• Subjects: 10X Genomics Chromium; Adaptation; Altitude; Analysis; Anser cygnoides; Anser indicus; Avian genomes; Bar-headed goose; Biochemistry; Comparative genomics; Conservation genomics; Deoxyribonucleic acid; DNA; DNA sequencing; Evolution & development; Geese; Gene families; Genes; Genetic research; Genomes; Genomics; High-altitude environments; Hypoxia; Metabolism; Migratory birds; Nucleotide sequence; Physiology; Population genetics; Population studies; Positive selection; Wetlands; Whole genome sequencing; Zoology; China; India; Conservation genomics; High-altitude adaptation; Positive selection; Qinghai-Tibetan Plateau; Comparative genomics; Hypoxia; Bar-headed goose; 10X Genomics Chromium; Anser indicus; Avian genomes
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.8914

The bar-headed goose (
) 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.
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.
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 (
), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau.
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.