How low can you go: sex identification from sequencing data of species lacking assembled sex chromosomes

Abstract

AbstractAccurate sex identification is crucial for elucidating the biology of a species. Here, we present SeXY, a sex-identification pipeline, for very low-coverage shotgun sequencing data from a single individual. The method does not require a conspecific sex-chromosome assembly as reference. SeXY was specifically designed to utilise low-effort screening data for sexing, but can also be applied to samples of higher-effort sequencing. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1,000 mapped reads, and mapping to a variety of reference genomes of various quality and phylogenetic distance. We show that when mapping to a high-quality (highly contiguous N50 > 30 Mb in our case, or chromosome-level) conspecific genome, our method is 100% accurate even down to 1,000 mapped reads. For lower-quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires data from only a single individual, (ii) does not require assembled conspecific sex-chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1,000 mapped reads in many cases. SeXY is broadly applicable to any target species with a heterogametic sex, including birds, mammals, and certain reptiles, fish, and insects.