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

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.

Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity

“…Although early comparisons of avian genomes were restricted to the chicken and zebra finch, where high level comparisons of synteny and karyotype led to the conclusion that bird genomes were largely stable compared with mammals ( Ellegren 2010 ), the discovery of many intrachromosomal rearrangements across birds ( Skinner and Griffin 2012 ; Zhang et al 2014 ; Farré et al 2016 ; Hooper and Price 2017 ) and interchromosomal recombination in falcons, parrots, and sandpipers ( O’Connor et al 2018 ; Coelho et al 2019 ; Pinheiro et al 2021 ) has shown that at a finer resolution for comparison, the avian genome is rather dynamic. The highly variable rate of TE expansion we have observed across birds extends knowledge from avian orders with “unusual” repeat landscapes, that is, Piciformes ( Manthey et al 2018 ) and Passeriformes ( Warren et al 2010 ), and provides further evidence that the genome evolution of bird orders and species within orders differs significantly, even though synteny is often conserved.…”

Genomic architecture drives population structuring in Amazonian birds

“…We obtained reference genomes from closely related species. For P. nigromaculata, we used as reference the genome of Rhegmatorhina melanosticta (Coelho et al 2019) with TMRCA = 9.60Ma (Harvey et al 2020). For X. spixii, we used the genome of X. elegans (GCA_013401175.1 ASM1340117v1; NCBI genome ID: 92877; Feng et al 2020) with TMRCA = 2.36Ma (Harvey et al 2020), and for L. vociferans we used the genome of Cephalopterus ornatus (GCA_013396775.1 ASM1339677v1; NCBI genome ID: 92752; Feng et al 2020) with TMRCA =15.10Ma (Harvey et al 2020).…”

Genome stability is in the eye of the beholder: recent retrotransposon activity varies significantly across avian diversity

“…While early comparisons of avian genomes were restricted to the chicken and zebra finch, where high level comparisons of synteny and karyotype led to the conclusion that bird genomes were largely stable compared to mammals (Ellegren 2010), the discovery of many intrachromosomal rearrangements across birds (Hooper and Price 2017;Skinner and Griffin 2012;Zhang et al 2014;Farre et al 2016) and interchromosomal recombination in falcons, parrots and sandpipers (O'Connor et al 2018;Coelho et al 2019;Pinheiro et al 2021) has shown that at a finer resolution for comparison, the avian genome is rather dynamic. The highly variable rate of TE expansion we have observed across birds extends knowledge from avian orders with "unusual" repeat landscapes, i.e., Piciformes (Manthey et al 2018) and Passeriformes (Warren et al 2010), and provides further evidence that the genome evolution of bird orders and species within orders differs significantly, even though synteny is often conserved.…”