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

Wen Wang; Fang Wang; Rongkai Hao; Aizhen Wang; Kirill Sharshov; Alexey Druzyaka; Zhuoma Lancuo; Yuetong Shi; Shuo Feng

doi:10.7717/peerj.8914

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

PeerJ. 2020 Apr 6:8:e8914. doi: 10.7717/peerj.8914. eCollection 2020.

Authors

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

Affiliations

¹ State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China.
² Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, Qinghai, China.
³ Novogene Bioinformatics Institute, Beijing, China.
⁴ College of Eco-Environmental Engineering, Qinghai University, Xi'ning, Qinghai, China.
⁵ Research Institute of Experimental and Clinical Medicine, Novosibirsk, Russia.
⁶ Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
⁷ School of Finance and Economics, Qinghai University, Xi'ning, Qinghai, China.
⁸ KunLun College of Qinghai University, Xi'ning, Qinghai, China.

Abstract

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.

Keywords: 10X Genomics Chromium; Anser indicus; Avian genomes; Bar-headed goose; Comparative genomics; Conservation genomics; High-altitude adaptation; Hypoxia; Positive selection; Qinghai-Tibetan Plateau.

Associated data

figshare/10.6084/m9.figshare.8229083.v1

Grants and funding

This research was funded by the National Natural Science Foundation of China (grant No. 31960277), the Natural Science Foundation of Qinghai Province of China (grant No. 2018-ZJ-932Q), the Project of Qinghai Science & Technology Department (grant No. 2016-ZJ-Y01), the Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University (grant No. 2017-ZZ-21) and the Project of Tao He Yuan National Wetland Park in Qinghai Province (grant No. 2018-THY-010203). Dr. Wen Wang and Shuo Feng were both supported by “1000 Talent” programs of Qinghai Province. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.