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

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

Wen Wang  1 , Fang Wang  2 , Rongkai Hao  3 , Aizhen Wang  4 , Kirill Sharshov  5 , Alexey Druzyaka  6 , Zhuoma Lancuo  7 , Yuetong Shi  8 , Shuo Feng  1
Affiliations

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

Wen Wang et al. PeerJ. .

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.

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Conflict of interest statement

The authors declare there are no competing interests. Rongkai Hao is employed by Novogene Bioinformatics Institute.

Figures

Figure 1
Figure 1. Orthologous genes in bar-headed goose and other birds.
The number of unique or shared orthologous genes are listed in each diagram component. Ain, bar-headed goose; Acy, swan goose; Apl, mallard; Gga, red junglefowl.
Figure 2
Figure 2. Gene family expansion and contraction in the bar-headed goose genome.
The number of expanded (blue) and contracted (red) gene families are shown along branches and nodes. MRCA, most recent common ancestor; Ain, bar-headed goose; Acy, swan goose; Nni, crested ibis; Apl, mallard; Gga, red junglefowl; Mga, turkey; Cca, common cuckoo; Cli, rock pigeon; Phu, ground tit; Cfl, bananaquit; Pma, great tit; Tgu, zebra finch; Ppu, ruff; Fpe, peregrine falcon; Bmu, yak; Pho, tibetan antelope.
Figure 3
Figure 3. Functional distribution of positively selected genes (PSGs) according to the Gene Ontology (GO) database.
The y axis reveals the GO functional categories, including (A) biological process, (B) cellular component, and (C) molecular function, while the number of genes in each category is plotted on the x axis.
See this image and copyright information in PMC

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