A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)

Laís Coelho,Lukas Musher,Joel Cracraft

doi:10.3390/d11090144

Laís Coelho, Lukas Musher + Show 1 more

Open Access

https://doi.org/10.3390/d11090144

Copy DOI

Journal: Diversity	Publication Date: Aug 23, 2019
Citations: 14	License type: CC BY 4.0

Affiliation: Columbia University, American Museum of Natural History

Abstract

Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.

Highlights

Organismal biology has been revolutionized over the past decade by the ‘omics’ era, in which the rapid development of high-throughput sequencing technologies has enabled the acquisition of more genetic data than ever before, including for non-model organisms [1]
We have demonstrated that linked-read technologies are valuable resources for generating high contiguity genomes, with relatively complete sequencing of putatively conserved genomic regions
The high completeness of our assembly relative to other publicly available genomes means that new data are available for incorporation into ongoing phylogenomic and population genomic work on avian evolution

Summary

Introduction

Organismal biology has been revolutionized over the past decade by the ‘omics’ era, in which the rapid development of high-throughput sequencing technologies has enabled the acquisition of more genetic data than ever before, including for non-model organisms [1]. The number of avian genomes available on GenBank has increased by more than tenfold over the past five years (from 11 [1] to 182 as of this writing) the total number is still relatively low; just under two percent of recognized avian species are represented compared with over 6% of mammals (see Bird10K project [2]). Lower still is the number of available avian genomes that are assembled to the chromosome-level (only 18 on GenBank as of this writing, most of which were de novo assembled)

Objectives

Methods

Discussion

Conclusion