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Open AccessArticle

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

1
Department of Ecology, Evolution and Environmental Biology, Columbia University, 10th floor Schermerhorn Building, 1200 Amsterdam Ave, New York, NY 10025, USA
2
Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
3
Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
*
Author to whom correspondence should be addressed.
Diversity 2019, 11(9), 144; https://doi.org/10.3390/d11090144
Received: 12 July 2019 / Revised: 16 August 2019 / Accepted: 21 August 2019 / Published: 23 August 2019
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
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. View Full-Text
Keywords: linked-read sequencing; genome completeness; contiguity; assembly; Tyranni linked-read sequencing; genome completeness; contiguity; assembly; Tyranni
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Coelho, L.A.; Musher, L.J.; Cracraft, J. A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae). Diversity 2019, 11, 144.

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