ArticleGenome research2013
Efficient identification of Y chromosome sequences in the human and Drosophila genomes.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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75 citing papers in PubMed, 141 citations in OpenAlex.
- Detection of sex chromosomes in Tephritid pests using R-CQ and KAMY, two computational methods to support generic pest management applications.Insect science · 2026Article
- CRISPR/Cas9-mediated mutagenesis of the white-eye gene in the tephritid pest Bactrocera zonata.Insect science · 2026Article
- Sex chromosome identification and genome curation from a single individual with SCINKD.Molecular biology and evolution · 2026Article
- Mosquito sex separation using complementation of selectable traits and engineered neo-sex chromosomes.Nature communications · 2025Article
- Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome.Molecular biology and evolution · 2025Article
- Male sterility in Drosophila mojavensis × D. arizonae hybrids is not caused by gene movements in the Y chromosome.Evolution; international journal of organic evolution · 2025Article
- Origin and evolutionary trajectories of brown algal sex chromosomes.Nature ecology & evolution · 2025Article
- Genetic diversity of the Y-chromosome in domestic animals: from evolutionary insights to functional implications.Molecular biology reports · 2025Review
- Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.G3 (Bethesda, Md.) · 2025Article
- Structural and evolutionary features of red algal UV sex chromosomes.Genome biology · 2025Article
- OligoY pipeline for full Y chromosome painting.Briefings in bioinformatics · 2025Article
- Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.Molecular ecology resources · 2025Article
- Sex Chromosome Evolution: Hallmarks and Question Marks.Molecular biology and evolution · 2024Review
- Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome.Zoological letters · 2024Article
- Why should we study plant sex chromosomes?The Plant cell · 2024Review
- High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.Genome biology and evolution · 2024Article
- Chromosome-Level Assembly of Artemia franciscana Sheds Light on Sex Chromosome Differentiation.Genome biology and evolution · 2024Article
- An effective strategy for assembling the sex-limited chromosome.GigaScience · 2024Article
- Can a Y Chromosome Degenerate in an Evolutionary Instant? A Commentary on Fong et al. 2023.Genome biology and evolution · 2023Article
- Parsimony and Poeciliid Sex Chromosome Evolution.Genome biology and evolution · 2023Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Notwithstanding their biological importance, Y chromosomes remain poorly known in most species. A major obstacle to their study is the identification of Y chromosome sequences; due to its high content of repetitive DNA, in most genome projects, the Y chromosome sequence is fragmented into a large number of small, unmapped scaffolds. Identification of Y-linked genes among these fragments has yielded important insights about the origin and evolution of Y chromosomes, but the process is labor intensive, restricting studies to a small number of species. Apart from these fragmentary assemblies, in a few mammalian species, the euchromatic sequence of the Y is essentially complete, owing to painstaking BAC mapping and sequencing. Here we use female short-read sequencing and k-mer comparison to identify Y-linked sequences in two very different genomes, Drosophila virilis and human. Using this method, essentially all D. virilis scaffolds were unambiguously classified as Y-linked or not Y-linked. We found 800 new scaffolds (totaling 8.5 Mbp), and four new genes in the Y chromosome of D. virilis, including JYalpha, a gene involved in hybrid male sterility. Our results also strongly support the preponderance of gene gains over gene losses in the evolution of the Drosophila Y. In the intensively studied human genome, used here as a positive control, we recovered all previously known genes or gene families, plus a small amount (283 kb) of new, unfinished sequence. Hence, this method works in large and complex genomes and can be applied to any species with sex chromosomes.
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