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 orcid.org/0000-0001-7987-738X
Falk, Stephanie
Morales, Hernan E.
Austin, Christopher M.ORCID iD for Austin, Christopher M. orcid.org/0000-0003-1848-6267
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
genome
neo-W
neo-Z
passerine
sex chromosome
songbird
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)
Persistent URL http://hdl.handle.net/10536/DRO/DU:30129717

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