DOI: 10.5061/dryad.280gb5mr6
title: Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

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 &gt;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.
description: Below are short descriptions of our methods.
 Please see our eLife paper for detailed methods.<br>
 <strong>Heterochromatin-sensitive genome
 assemblies:</strong><br> We created new genome assemblies for
 D. simulans, D. sechellia, and D. mauritiana using the
 heterochromatin-sensitive assembly pipeline from Chang and Larracuente
 2019. We polished the resulting assemblies once with Quiver using PacBio
 reads (SMRT Analysis v2.3.0) and ten times with Pilon v1.22  using raw
 Illumina reads with parameters “--mindepth 3 --minmq 10 --fix bases”. We
 also used Repeatmasker v4.0.5 with a ​​custom repeat library to search
 repetitive sequences in our assemblies<br> <strong>Repeat
 library:</strong><br> We modified the repeat library from
 Chakraborty et al. 2021, by adding the consensus sequence of Jockey-3 from
 D. melanogaster to replace its homologs (G2 in D. melanogaster and
 Jockey-3 in D. simulans; Chang et al. 2019).<br> <strong>Gene
 annotation:</strong><br> To annotate the genomes, we collected
 Iso-seq from D. simulans and translated sequences from D. melanogaster and
 mapped these sequences to the genomes using MAKER2. We also mapped RNA-seq
 data from different tissues using STAR 2.7.3a and combined the annotation
 using Stringtie 2.0.3. We further improved the mitochondria annotation
 using MITOS2.<br> <strong>Indel and gene conversion
 alignments:</strong><br> We extracted Y-linked sequences using
 BLASTN, and aligned them using Geneious with manual curation. We
 calculated the gene conversion rate using compute with methods from Chang
 and Larracuente 2019. and surveyed the indel sizes using these
 alignments. <b id="docs-internal-guid-05bc4e26-7fff-9f96-1831-4159a5001c7d">References:</b> Chang CH, Larracuente AM. Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome. Genetics. 2019;211(1):333-48. Epub 2018/11/14. doi: 10.1534/genetics.118.301765. PubMed PMID: 30420487; PubMed Central PMCID: PMCPMC6325706.<br> Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, et al. Evolution of genome structure in the Drosophila simulans species complex. Genome research. 2021;31(3):380-96. Epub 2021/02/11. doi: 10.1101/gr.263442.120. PubMed PMID: 33563718; PubMed Central PMCID: PMCPMC7919458.<br> Chang CH, Chavan A, Palladino J, Wei X, Martins NMC, Santinello B, et al. Islands of retroelements are major components of Drosophila centromeres. PLoS Biol. 2019;17(5):e3000241. Epub 2019/05/16. doi: 10.1371/journal.pbio.3000241. PubMed PMID: 31086362; PubMed Central PMCID: PMCPMC6516634.
description: 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<br>
 dsec_scaffold2_V2.fasta – D. sechellia genome assembly<br>
 dmau_scaffold2_V2.fasta – D. mauritiana genome assembly<br>
 dsim_scaffold2_V2.fasta.out – Repeatmasker output of D. simulans genome
 assembly<br> dsec_scaffold2_V2.fasta.out – Repeatmasker output of D.
 sechellia genome assembly<br> dmau_scaffold2_V2.fasta.out –
 Repeatmasker output of D. mauritiana genome assembly<br> Gene
 annotation.zip – gene annotation for three species (gtf files)<br>
 Repeat_library.fasta – Repeat library sequences used in this
 study<br> PAML.zip – Alignments and trees used for our PAML analyses
 in Fig 6<br> Gene_conversion_alignment.zip – Raw indel alignments
 for calculating gene conversion rate<br> Indel_align.zip – Raw indel
 alignments for Fig 7 <br> Ching-Ho_simY_FISH.zip – raw FISH and
 immuno-FISH microscope images<br>