Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution.

Genome Biology
Catherine L PeichelMichael A. White

Abstract

Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to degeneration of the Y chromosome. The progression of degeneration is not well understood, as complete sequence assemblies of heteromorphic Y chromosomes have only been generated across a handful of taxa with highly degenerate sex chromosomes. Here, we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old and at an intermediate stage of degeneration. Our previous work identified that the non-recombining region between the X and the Y spans approximately 17.5 Mb on the X chromosome. We combine long-read sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome BAC clones. We find three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The threespine stickleback Y shows convergence with more degenerate sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with t...Continue Reading

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Citations

Sep 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Nima RafatiLeif Andersson
Oct 30, 2020·Journal of Evolutionary Biology·Emma L BerdanGenevieve M Kozak
Dec 11, 2020·Molecular Biology and Evolution·Matthew A ConteThomas D Kocher
Dec 17, 2020·Molecular Ecology Resources·Annabel WhibleyShawn R Narum
Feb 19, 2021·G3 : Genes - Genomes - Genetics·Shivangi NathMichael A White
Feb 17, 2021·Evolution; International Journal of Organic Evolution·Deborah Charlesworth
Apr 20, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Aline MuyleJames M A Turner
Jul 13, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Qiaowei PanAmaury Herpin
Jul 27, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Lukáš KratochvílMartina Johnson Pokorná
Jul 27, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Alexandr SemberMarcelo de Bello Cioffi
Jun 13, 2021·Molecular Biology and Evolution·Jason M SardellMark Kirkpatrick
Aug 10, 2021·PLoS Genetics·Deborah CharlesworthKaren Keegan
Apr 29, 2021·Annual Review of Genomics and Human Genetics·Kerry ReidKrishna R Veeramah

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Datasets Mentioned

BETA
SRR6954368
SRR6954338
SRR5626528
SRR5626529
AAH49194.1
AAX81416.1

Methods Mentioned

BETA
Hi-C
immunoprecipitation
ChIP-seq
genotyping
RNA-seq

Software Mentioned

gffread
genomecov package of bedtools
custom
MarkDuplicates of Picard Tools
Juicer
RepeatMasker
Ensembl
Bioconductor package
Cufflinks
edgeR

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