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Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
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2020 (English)In: BMC Biology, E-ISSN 1741-7007, Vol. 18, no 1, article id 78Article in journal (Refereed) Published
Abstract [en]

Background: Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.

Results: Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.

Conclusions: Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

Place, publisher, year, edition, pages
Springer Nature, 2020. Vol. 18, no 1, article id 78
Keywords [en]
Sex chromosomes, W-chromosome, Recombination suppression, Willow, Salix
National Category
Genetics and Breeding in Agricultural Sciences
Identifiers
URN: urn:nbn:se:umu:diva-173793DOI: 10.1186/s12915-020-00808-1ISI: 000546932800002PubMedID: 32605573Scopus ID: 2-s2.0-85087385837OAI: oai:DiVA.org:umu-173793DiVA, id: diva2:1456302
Funder
Swedish Research Council Formas, 2016-20031Swedish Energy Agency, 30599-5EU, European Research Council, 260233EU, European Research Council, 680951Available from: 2020-08-04 Created: 2020-08-04 Last updated: 2024-01-17Bibliographically approved

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Churcher, Allison M

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CiteExportLink to record
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