Genomic evidence of neo-sex chromosomes in the eastern yellow robin

Gan, Han Ming, Falk, Stephanie, Morales, Hernan E., Austin, Christopher M., Sunnucks, Paul and Pavlova, Alexandra 2019, Genomic evidence of neo-sex chromosomes in the eastern yellow robin, GigaScience, vol. 8, no. 9, pp. 1-10, doi: 10.1093/gigascience/giz111.

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Title Genomic evidence of neo-sex chromosomes in the eastern yellow robin
Author(s) Gan, Han MingORCID iD for Gan, Han Ming
Falk, Stephanie
Morales, Hernan E.
Austin, Christopher M.ORCID iD for Austin, Christopher M.
Sunnucks, Paul
Pavlova, Alexandra
Journal name GigaScience
Volume number 8
Issue number 9
Start page 1
End page 10
Total pages 10
Publisher Oxford University Press
Place of publication Oxford, Eng.
Publication date 2019-09
ISSN 2047-217X
Keyword(s) Eopsaltria australis
W chromosome
eastern yellow robin
sex chromosome
Eopsaltria australis
Summary BACKGROUND: Understanding sex-biased natural selection can be enhanced by access to well-annotated chromosomes including ones inherited in sex-specific fashion. The eastern yellow robin (EYR) is an endemic Australian songbird inferred to have experienced climate-driven sex-biased selection and is a prominent model for studying mitochondrial-nuclear interactions in the wild. However, the lack of an EYR reference genome containing both sex chromosomes (in birds, a female bearing Z and W chromosomes) limits efforts to understand the mechanisms of these processes. Here, we assemble the genome for a female EYR and use low-depth (10×) genome resequencing data from 19 individuals of known sex to identify chromosome fragments with sex-specific inheritance. FINDINGS: MaSuRCA hybrid assembly using Nanopore and Illumina reads generated a 1.22-Gb EYR genome in 20,702 scaffolds (94.2% BUSCO completeness). Scaffolds were tested for W-linked (female-only) inheritance using a k-mer approach, and for Z-linked inheritance using median read-depth test in male and female reads (read-depths must indicate haploid female and diploid male representation). This resulted in 2,372 W-linked scaffolds (total length: 97,872,282 bp, N50: 81,931 bp) and 586 Z-linked scaffolds (total length: 121,817,358 bp, N50: 551,641 bp). Anchoring of the sex-linked EYR scaffolds to the reference genome of a female zebra finch revealed 2 categories of sex-linked genomic regions. First, 653 W-linked scaffolds (25.7 Mb) were anchored to the W sex chromosome and 215 Z-linked scaffolds (74.4 Mb) to the Z. Second, 1,138 W-linked scaffolds (70.9 Mb) and 179 Z-linked scaffolds (51.0 Mb) were anchored to a large section (coordinates ∼5 to ∼60 Mb) of zebra finch chromosome 1A. The first ∼5 Mb and last ∼14 Mb of the reference chromosome 1A had only autosomally behaving EYR scaffolds mapping to them. CONCLUSIONS: We report a female (W chromosome-containing) EYR genome and provide genomic evidence for a neo-sex (neo-W and neo-Z) chromosome system in the EYR, involving most of a large chromosome (1A) previously only reported to be autosomal in passerines.
Language eng
DOI 10.1093/gigascience/giz111
Indigenous content off
HERDC Research category C1 Refereed article in a scholarly journal
Copyright notice ©2019, The Author(s)
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