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Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

Mutti, Giacomo, Oteo-Garcia, Gonzalo, Caldon, Matteo, da Silva, Maria Joana Ferreira, Minhós, Tânia, Cowlishaw, Guy, Gottelli, Dada, Huchard, Elise, Carter, Alecia, Martinez, Felipe I., Raveane, Alessandro and Capelli, Cristian 2023. Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes. Scientific Reports 13 (1) , 13839. 10.1038/s41598-023-40931-x

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Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Biosciences
Additional Information: License information from Publisher: LICENSE 1: URL:, Type: open-access
Publisher: Nature Research
ISSN: 2045-2322
Date of First Compliant Deposit: 25 August 2023
Date of Acceptance: 18 August 2023
Last Modified: 08 Oct 2023 05:12

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