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The majority of nematode species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX\/X0). Some filarial nematode species, including important parasites of humans, have heteromorphic XX\/XY karyotypes. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused homologue of an autosome involved in an X-autosome fusion event. Here, we generated a chromosome-level reference genome for <jats:italic>Litomosoides sigmodontis<\/jats:italic>, a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX\/X0). By mapping the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements, we infer that the ancestral filarial X chromosome was the product of a fusion between NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal). In the two filarial lineages with XY systems, there have been two independent X-autosome chromosome fusion events involving different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from the unfused homologue of the autosome. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a Y-linked sex-determining locus.<\/jats:p>","DOI":"10.1371\/journal.pgen.1011116","type":"journal-article","created":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T18:31:06Z","timestamp":1705429866000},"page":"e1011116","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":11,"title":["The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6075-8273","authenticated-orcid":true,"given":"Lewis","family":"Stevens","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuela","family":"Kieninger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Chan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7545-2162","authenticated-orcid":true,"given":"Jonathan M. 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Post","year":"1989","journal-title":"Trop Med Parasitol"},{"key":"pgen.1011116.ref033","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1534\/genetics.110.124958","article-title":"An asymmetric chromosome pair undergoes synaptic adjustment and crossover redistribution during Caenorhabditis elegans meiosis: implications for sex chromosome evolution","volume":"187","author":"JV Henzel","year":"2011","journal-title":"Genetics"},{"key":"pgen.1011116.ref034","doi-asserted-by":"crossref","first-page":"911","DOI":"10.2307\/2408899","article-title":"THE ACCUMULATION OF SEXUALLY ANTAGONISTIC GENES AS A SELECTIVE AGENT PROMOTING THE EVOLUTION OF REDUCED RECOMBINATION BETWEEN PRIMITIVE SEX CHROMOSOMES","volume":"41","author":"WR Rice","year":"1987","journal-title":"Evolution"},{"key":"pgen.1011116.ref035","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1016\/j.tig.2018.04.001","article-title":"Why Do Sex Chromosomes Stop Recombining?","volume":"34","author":"S Ponnikas","year":"2018","journal-title":"Trends Genet"},{"key":"pgen.1011116.ref036","doi-asserted-by":"crossref","first-page":"e3001698","DOI":"10.1371\/journal.pbio.3001698","article-title":"Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes","volume":"20","author":"P Jay","year":"2022","journal-title":"PLoS Biol"},{"key":"pgen.1011116.ref037","doi-asserted-by":"crossref","first-page":"1342","DOI":"10.3390\/ani12111342","article-title":"De Novo Assembly of the Dirofilaria immitis Genome by Long-Read Nanopore-Based Sequencing Technology on an Adult Worm from a Canine Cardiopulmonary Dirofilariosis Case","volume":"12","author":"S Gomes-de-S\u00e1","year":"2022","journal-title":"Animals"},{"key":"pgen.1011116.ref038","doi-asserted-by":"crossref","first-page":"e1007770","DOI":"10.1371\/journal.pgen.1007770","article-title":"An investigation of Y chromosome incorporations in 400 species of Drosophila and 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Goswami","year":"1978","journal-title":"Curr Sci"},{"key":"pgen.1011116.ref042","doi-asserted-by":"crossref","first-page":"3239","DOI":"10.1038\/s41467-022-30578-z","article-title":"Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms","volume":"13","author":"Y Wang","year":"2022","journal-title":"Nat Commun"},{"key":"pgen.1011116.ref043","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/j.tig.2005.08.003","article-title":"Comparative genomics of nematodes","volume":"21","author":"M Mitreva","year":"2005","journal-title":"Trends Genet"},{"key":"pgen.1011116.ref044","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/j.ympev.2011.07.007","article-title":"Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species","volume":"61","author":"DR Denver","year":"2011","journal-title":"Mol Phylogenet Evol"},{"key":"pgen.1011116.ref045","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s12864-022-08375-1","article-title":"HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly","volume":"23","author":"SB Sim","year":"2022","journal-title":"BMC Genomics"},{"key":"pgen.1011116.ref046","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"G Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"key":"pgen.1011116.ref047","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes","volume":"11","author":"TR Ranallo-Benavidez","year":"2020","journal-title":"Nat Commun"},{"key":"pgen.1011116.ref048","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"H Cheng","year":"2021","journal-title":"Nat Methods"},{"key":"pgen.1011116.ref049","first-page":"10","article-title":"Twelve years of SAMtools and BCFtools","author":"P Danecek","year":"2021","journal-title":"Gigascience"},{"key":"pgen.1011116.ref050","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"H. Li","year":"2013","journal-title":"arXiv [q-bio.GN]."},{"key":"pgen.1011116.ref051","first-page":"39","article-title":"YaHS: yet another Hi-C scaffolding tool","author":"C Zhou","year":"2023","journal-title":"Bioinformatics"},{"key":"pgen.1011116.ref052","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1534\/g3.119.400908","article-title":"BlobToolKit\u2013Interactive Quality Assessment of Genome Assemblies","volume":"10","author":"R Challis","year":"2020","journal-title":"G3 Genes|Genomes|Genetics"},{"key":"pgen.1011116.ref053","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1186\/s12859-023-05385-y","article-title":"MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads","volume":"24","author":"Darwin Tree of Life Consortium","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"pgen.1011116.ref054","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies","volume":"36","author":"D Guan","year":"2020","journal-title":"Bioinformatics"},{"key":"pgen.1011116.ref055","doi-asserted-by":"crossref","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA\/Q File Manipulation","volume":"11","author":"W Shen","year":"2016","journal-title":"PLoS One"},{"key":"pgen.1011116.ref056","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies","volume":"21","author":"A Rhie","year":"2020","journal-title":"Genome Biol"},{"key":"pgen.1011116.ref057","doi-asserted-by":"crossref","first-page":"2508","DOI":"10.1093\/bioinformatics\/btw159","article-title":"gEVAL\u2014a web-based browser for evaluating genome assemblies","volume":"32","author":"W Chow","year":"2016","journal-title":"Bioinformatics"},{"key":"pgen.1011116.ref058","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","article-title":"Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments","volume":"3","author":"NC Durand","year":"2016","journal-title":"Cell Syst"},{"key":"pgen.1011116.ref059","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"H. Li","year":"2018","journal-title":"Bioinformatics"},{"key":"pgen.1011116.ref060","first-page":"247148","article-title":"Assembly of Long Error-Prone Reads Using Repeat Graphs","author":"M Kolmogorov","year":"2018","journal-title":"bioRxiv"},{"key":"pgen.1011116.ref061","first-page":"6","article-title":"Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm","author":"E Lefoulon","year":"2020","journal-title":"Microb Genom"},{"key":"pgen.1011116.ref062","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T. Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"pgen.1011116.ref063","doi-asserted-by":"crossref","first-page":"e3001972","DOI":"10.1371\/journal.pbio.3001972","article-title":"Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project","volume":"21","author":"E Vancaester","year":"2023","journal-title":"PLoS Biol"},{"key":"pgen.1011116.ref064","article-title":"Earl Grey: a fully automated user-friendly transposable element annotation and analysis pipeline.","author":"T Baril","year":"2022"},{"key":"pgen.1011116.ref065","author":"AFA Smit","year":"2015","journal-title":"RepeatMasker Open-4.0. 2013\u20132015"},{"key":"pgen.1011116.ref066","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"pgen.1011116.ref067","first-page":"3","article-title":"BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database","author":"T Br\u016fna","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"pgen.1011116.ref068","doi-asserted-by":"crossref","first-page":"D445","DOI":"10.1093\/nar\/gkac998","article-title":"OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity","volume":"51","author":"D Kuznetsov","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"pgen.1011116.ref069","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1186\/s12859-021-04482-0","article-title":"TSEBRA: transcript selector for BRAKER","volume":"22","author":"L Gabriel","year":"2021","journal-title":"BMC 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