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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; ... Capelli, Cristian; + view all (2023) Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes. Scientific Reports , 13 (1) , Article 13839. 10.1038/s41598-023-40931-x. Green open access

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Abstract

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.

Type: Article
Title: Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/s41598-023-40931-x
Publisher version: https://doi.org/10.1038/s41598-023-40931-x
Language: English
Additional information: This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third-party material in this article are included in the Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Keywords: Humans, Male, Animals, Metagenomics, Theropithecus, Papio, Macaca mulatta, Microsatellite Repeats
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL SLASH
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Dept of Anthropology
URI: https://discovery.ucl.ac.uk/id/eprint/10175995
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