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

Humans Male Animals Metagenomics Theropithecus Papio Macaca mulatta Microsatellite Repeats / genetics

Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
24 08 2023
Historique:
received: 03 04 2023
accepted: 18 08 2023
medline: 28 8 2023
pubmed: 25 8 2023
entrez: 24 8 2023
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41598-023-40931-x PMID: 37620368 PMC: PMC10449864
pubmed: 37620368
doi: 10.1038/s41598-023-40931-x
pii: 10.1038/s41598-023-40931-x
pmc: PMC10449864
doi:

Banques de données

figshare
['10.6084/m9.figshare.23810817.v2']

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

13839

Informations de copyright

© 2023. Springer Nature Limited.

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Auteurs

Giacomo Mutti (G)

Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy.
Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain.
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.

Gonzalo Oteo-Garcia (G)

Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy.

Matteo Caldon (M)

Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy.

Maria Joana Ferreira da Silva (MJF)

BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
Centro de Investigação Em Biodiversidade E Recursos Genéticos, CIBIOInBIO Laboratório AssociadoUniversidade Do Porto, Campus de Vairão, Vairão, Portugal.
ONE ‑ Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK.

Tânia Minhós (T)

Centre for Research in Anthropology (CRIA-NOVA FCSH), Av. Forças Armadas, Edifício ISCTE, Sala 2w2, 1649-026, Lisboa, Portugal.
Anthropology Department, School of Social Sciences and Humanities, Universidade Nova de Lisboa (NOVA FCSH), Av. de Berna, 26-C, 1069-061, Lisboa, Portugal.

Guy Cowlishaw (G)

Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.

Dada Gottelli (D)

Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.

Elise Huchard (E)

Institut Des Sciences de L'Evolution, CNRS, Universite de Montpellier, CC 065, 34095, Montpellier 05, France.

Alecia Carter (A)

Department of Anthropology, University College London, 14 Taviton Street, London, WC1H 0BW, UK.

Felipe I Martinez (FI)

Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile.

Alessandro Raveane (A)

Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.

Cristian Capelli (C)

Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy. cristian.capelli@unipr.it.
Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK. cristian.capelli@unipr.it.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Assessing the recovery of Y chromosome...
questionsmedicales.fr › Eucaryotes › Animaux › Assessing the recovery of Y chromosome...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Métagénomique › Assessing the recovery of Y chromosome...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Cercopithecidae › Cercopithecinae › Theropithecus › Assessing the recovery of Y chromosome...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Cercopithecidae › Cercopithecinae › Papio › Assessing the recovery of Y chromosome...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Cercopithecidae › Cercopithecinae › Macaca › Macaca mulatta › Assessing the recovery of Y chromosome...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées en tandem › Répétitions microsatellites › Assessing the recovery of Y chromosome...