Journal article
A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)
Diversity (Basel), v 11(9), 144
01 Sep 2019
Featured in Collection : UN Sustainable Development Goals @ Drexel
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 10x) 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.
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Details
- Title
- A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae)
- Creators
- Lais A. Coelho - Columbia UniversityLukas J. Musher - American Museum of Natural HistoryJoel Cracraft - American Museum of Natural History
- Publication Details
- Diversity (Basel), v 11(9), 144
- Publisher
- MDPI
- Number of pages
- 18
- Grant note
- 1146423 / NSF; National Science Foundation (NSF) 1241066 / NSF/NASA; National Science Foundation (NSF); National Aeronautics & Space Administration (NASA) 1146423 / Division Of Environmental Biology; Direct For Biological Sciences; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) BEX 1191136 / Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior - Brasil (CAPES); Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) Linda Gormezano Fund (American Museum of Natural History) F.M. Chapman Fund
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Ornithology
- Web of Science ID
- WOS:000487944500006
- Scopus ID
- 2-s2.0-85072102766
- Other Identifier
- 991022048280104721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Biodiversity Conservation
- Ecology