Dryad
Published May 22, 2022 | Version v1
Dataset Open

Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

Creators

  • 1. University of Rochester
  • 2. Cornell University
  • 3. University of Nebraska-Lincoln

Description

Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.

Notes

Please cite our eLife paper if you want to reuse the data. You can contact Ching-Ho Chang (hilynano@gmail.com) and Amanda Larracuente (alarracu@ur.rochester.edu) for any questions about the datasets

dsim_scaffold2_V2.fasta  – D. simulans genome assembly
dsec_scaffold2_V2.fasta – D. sechellia genome assembly
dmau_scaffold2_V2.fasta – D. mauritiana genome assembly
dsim_scaffold2_V2.fasta.out – Repeatmasker output of D. simulans genome assembly
dsec_scaffold2_V2.fasta.out – Repeatmasker output of D. sechellia genome assembly
dmau_scaffold2_V2.fasta.out – Repeatmasker output of D. mauritiana genome assembly
Gene annotation.zip – gene annotation for three species (gtf files)
Repeat_library.fasta – Repeat library sequences used in this study
PAML.zip – Alignments and trees used for our PAML analyses in Fig 6
Gene_conversion_alignment.zip – Raw indel alignments for calculating gene conversion rate
Indel_align.zip – Raw indel alignments for Fig 7 
Ching-Ho_simY_FISH.zip – raw FISH and immuno-FISH microscope images
 

Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: R35GM119515

Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: R01GM123194

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: MCB 1844693

Funding provided by: Damon Runyon Cancer Research Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100001021
Award Number: DRG: 2438-21

Funding provided by: UNL | College of Arts and Sciences, University of Nebraska-Lincoln (CAS)
Crossref Funder Registry ID:
Award Number:

Funding provided by: Ministry of Education, Taiwan*
Crossref Funder Registry ID:
Award Number:

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Additional details

Related works

Is cited by
10.1101/2021.08.16.456461 (DOI)
10.7554/eLife.75795.sa0 (DOI)