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

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

doi:10.7717/peerj.8914

Abstract

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.

Highlights

High-altitude environments impose severe physiological challenges on vertebrates, owing to the decrease in oxygen, pressure, and temperature relative to lowland habitats
We evaluated the completeness of the bar-headed goose genome assembly using Core Eukaryotic Genes Mapping Approach software (CEGMA), which compared a set of 248 core eukaryotic genes to the assembled sequence (Parra, Bradnam & Korf, 2007)
Using CEGMA on our assembly, we found that 211 conserved genes (85.08%) in bar-headed goose genome were successfully assembled, when compared to the 248 evolutionarily conserved core gene sets from six eukaryotic model organisms (Table S3)

Summary

Introduction

High-altitude environments impose severe physiological challenges on vertebrates, owing to the decrease in oxygen, pressure, and temperature relative to lowland habitats. One of the most well-known high-altitude bird species is the bar-headed goose (Anser indicus). Bar-headed geese can sustain the high metabolic rates and the high rates of oxygen consumption needed for flapping flight in severe hypoxia during their migration across the Himalayas (Ward et al, 2002). This species has become renowned for an example of high-altitude adaptation. 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 data will be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the barheaded geese at the genomic level

Methods

Results

Conclusion