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A W-linked palindrome and gene conversion in New World sparrows and blackbirds

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Abstract

A hallmark feature of the male-specific region of the human Y chromosome is the presence of large and near-identical palindromes. These palindromes are maintained in a state of near identity via gene conversion between the arms of the palindrome, and both neutral and selection-based theories have been proposed to explain their enrichment on the human Y and X chromosomes. While those proposed theories would be applicable to sex chromosomes in other species, it has not been established whether near-identical palindromes are a common feature of sex chromosomes in a broader range of taxa, including other tetrapods. Here, we report the genomic sequencing and features of a 279-kb region of the non-recombining portion of the W chromosome spanning the CHD1W locus in a New World sparrow, the white-throated sparrow (Zonotrichia albicollis), and the corresponding region on the Z chromosome. As has been observed for other Y and W chromosomes, we detected a high repetitive element content (51%) and low gene content on the white-throated sparrow W chromosome. In addition, we identified a 22-kb near-identical (>99%) palindrome on the W chromosome that flanks the 5′ end of the CHD1W gene. Signatures of gene conversion were readily detected between the arms of this palindrome, as was the presence of this palindrome in other New World sparrows and blackbirds. Near-identical palindromes are therefore present on the avian W chromosome and may persist due to the same forces proposed for the enrichment of these elements on the human sex chromosomes.

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Abbreviations

BAC:

Bacterial artificial chromosome

CHD1W:

Chromo-helicase DNA-binding protein, W chromosome

CHD1Z:

Chromo-helicase DNA-binding protein, Z chromosome

CHORI:

Children’s Hospital Oakland Research Institute

dNTP:

deoxy-nucleotide triphosphate

HINTW:

Histidine triad nucleotide binding protein W

kb:

Kilobase pairs

MSCI:

Meiotic sex chromosome inactivation

MSY:

Male-specific region of the Y chromosome

PCR:

Polymerase chain reaction

RASA1:

RAS p21 protein activator (GTPase activating protein) 1

RGMB:

RGM domain family, member B

UWBM:

University of Washington Burke Museum

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Acknowledgements

The authors thank Judith E. Mank for helpful comments and discussions, Mario Cáceres for comments, Cheryl T. Strauss for technical writing edits, Donna L. Maney for the dark-eyed junco DNA, Greg K. Tharp for computer support, the BC Cancer Agency Genome Sciences Centre, Vancouver, Canada, for generation of the BAC-end sequences, and members of the NIH Sequencing Center including E.D. Green, R. Blakesley, G. Bouffard, and J. McDowell. DNA samples (excluding the dark-eyed junco) were provided by The Burke Museum of Natural History and Culture. J.K.D. and J.W.T. were supported by a grant from the National Institutes of Health (1R21MH082046), and the NIH Intramural Sequencing Center was supported in part by the Intramural Research Program of the National Human Genome Research Institute of the National Institutes of Health.

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Authors and Affiliations

  1. Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA

    Jamie K. Davis & James W. Thomas

  2. Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA

    Pamela J. Thomas

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  1. Jamie K. Davis
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NISC Comparative Sequencing Program

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Correspondence to James W. Thomas.

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Responsible Editor: Mary E. Delany

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Davis, J.K., Thomas, P.J., NISC Comparative Sequencing Program. et al. A W-linked palindrome and gene conversion in New World sparrows and blackbirds. Chromosome Res 18, 543–553 (2010). https://doi.org/10.1007/s10577-010-9134-y

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