ArticleGenome biology and evolution2016
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms.
Article in Genome biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Silene, a versatile model system: from sex and genome evolution to ecology and speciation.The New phytologist · 2026Review
- An X-linked sex determination mechanism in cannabis and hop.Nature communications · 2026Article
- Unique sex chromosome translocations and evolutionary strata in two Sylvioidea songbird families.BMC genomics · 2026Article
- Evolution of Sex-Biased Gene Expression During Transitions to Separate Sexes in the Silene Genus.Molecular biology and evolution · 2025Article
- EASYstrata: an all-in-one workflow for genome annotation and genomic divergence analysis.NAR genomics and bioinformatics · 2025Article
- An X-linked sex determination mechanism in cannabis and hop.bioRxiv : the preprint server for biology · 2025Article
- The fourspine stickleback (Apeltes quadracus) has an XY sex chromosome system with polymorphic inversions on both X and Y chromosomes.PLoS genetics · 2025Article
- TheScience (New York, N.Y.) · 2025Article
- Sex Chromosome Evolution: Hallmarks and Question Marks.Molecular biology and evolution · 2024Review
- Sexy ways: approaches to studying plant sex chromosomes.Journal of experimental botany · 2024Review
- Evidence for feminized genetic males in a flea beetle using newly identified X-linked markers.Ecology and evolution · 2024Article
- Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes.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
- Evolutionary History of the Poecilia picta Sex Chromosomes.Genome biology and evolution · 2023Article
- Representing sex chromosomes in genome assemblies.Cell genomics · 2022Article
- Labile sex expression in angiosperm species with sex chromosomes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Dosage compensation evolution in plants: theories, controversies and mechanisms.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- The evolution of huge Y chromosomes inPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.BMC genomics · 2022Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical Silene data show that our method identifies 20-35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Approximately 12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY vs. ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimized for sex chromosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for our method. SEX-DETector and its implementation in a Galaxy workflow are made freely available.
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