{"doi":"10.7554/elife.75795","title":"Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes","abstract":"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.","journal":"eLife","year":2022,"id":246078,"datarank":1.2764909161171607,"base_score":3.8066624897703196,"endowment":3.8066624897703196,"self_citation_contribution":0.5709993734655481,"citation_network_contribution":0.7054915426516125,"self_endowment_contribution":0.5709993734655481,"citer_contribution":0.7054915426516125,"corpus_percentile":null,"corpus_rank":null,"citation_count":44,"citer_count":44,"citers_with_citation_signal":33,"citers_with_endowment":33,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9479,"is_data_producer":true,"deposit_databanks":{"Dryad":["10.5061/dryad.280gb5mr6"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":817779,"name":"Lauren E Gregory","orcid":"0000-0001-9766-998X","position":1,"is_corresponding":false},{"id":817780,"name":"Kathleen E Gordon","orcid":"0000-0003-2457-4554","position":2,"is_corresponding":false},{"id":509973,"name":"Colin D. Meiklejohn","orcid":"0000-0003-2708-8316","position":3,"is_corresponding":false},{"id":289357,"name":"Amanda M. Larracuente","orcid":"0000-0001-5944-5686","position":4,"is_corresponding":false},{"id":557279,"name":"Ching-Ho Chang","orcid":"0000-0001-9361-1190","position":0,"is_corresponding":true}],"reference_count":167,"raw_metadata":null,"created_at":"2026-07-19T00:23:43.438539Z","pmid":"34989337","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}