ArticleBMC genomics2022
Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Selective Regimes and Evolutionary Dynamics of Z and W Gametologs Across an Expanded Avian Neo-Sex Chromosome.Genome biology and evolution · 2026Article
- Widespread introgression and a potential role for a neo-sex chromosome in booby diversification and speciation.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary dynamics of enlarged neo-sex chromosomes and novel pseudoautosomal regions in Sylvioidea songbirds.Communications biology · 2026Article
- Rapid turnover of sex-determining architecture in invasive mussels.bioRxiv : the preprint server for biology · 2026Article
- Unique sex chromosome translocations and evolutionary strata in two Sylvioidea songbird families.BMC genomics · 2026Article
- Telomere-to-telomere reference genome of the common five-lined skink, Plestiodon fasciatus (Squamata: Scincidae).G3 (Bethesda, Md.) · 2026Article
- Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae).Genome biology and evolution · 2025Article
- Chromosome-level genome assembly of Dynastes reidi reveals structural evolution of autosomes and the sex chromosomes in Hercules beetles.G3 (Bethesda, Md.) · 2025Article
- EASYstrata: an all-in-one workflow for genome annotation and genomic divergence analysis.NAR genomics and bioinformatics · 2025Article
- Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.Molecular ecology · 2024Article
- Sex Chromosome Evolution: Hallmarks and Question Marks.Molecular biology and evolution · 2024Review
- A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay (Aphelocoma coerulescens).G3 (Bethesda, Md.) · 2024Article
- Sexy ways: approaches to studying plant sex chromosomes.Journal of experimental botany · 2024Review
- 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
- Evolutionary History of the Poecilia picta Sex Chromosomes.Genome biology and evolution · 2023Article
- A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds.Journal of evolutionary biology · 2022Article
- Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.Journal of evolutionary biology · 2022Article
- Genomic trajectories of a near-extinction event in the Chatham Island black robin.BMC genomics · 2022Article
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3 authors.
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Abstract
backgroundSex chromosomes have evolved numerous times, as revealed by recent genomic studies. However, large gaps in our knowledge of sex chromosome diversity across the tree of life remain. Filling these gaps, through the study of novel species, is crucial for improved understanding of why and how sex chromosomes evolve. Characterization of sex chromosomes in already well-studied organisms is also important to avoid misinterpretations of population genomic patterns caused by undetected sex chromosome variation.
resultsHere we present findZX, an automated Snakemake-based computational pipeline for detecting and visualizing sex chromosomes through differences in genome coverage and heterozygosity between any number of males and females. A main feature of the pipeline is the option to perform a genome coordinate liftover to a reference genome of another species. This allows users to inspect sex-linked regions over larger contiguous chromosome regions, while also providing important between-species synteny information. To demonstrate its effectiveness, we applied findZX to publicly available genomic data from species belonging to widely different taxonomic groups (mammals, birds, reptiles, and fish), with sex chromosome systems of different ages, sizes, and levels of differentiation. We also demonstrate that the liftover method is robust over large phylogenetic distances (> 80 million years of evolution).
conclusionsWith findZX we provide an easy-to-use and highly effective tool for identification of sex chromosomes. The pipeline is compatible with both Linux and MacOS systems, and scalable to suit different computational platforms.
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