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

dc.contributor.authorMutti, Giacomo
dc.contributor.authorOteo-Garcia, Gonzalo
dc.contributor.authorCaldon, Matteo
dc.contributor.authorFerreira da Silva, Maria Joana
dc.contributor.authorMinhós, Tânia
dc.contributor.authorCowlishaw, Guy
dc.contributor.authorGottelli, Dada
dc.contributor.authorHuchard, Elise
dc.contributor.authorCarter, Alecia
dc.contributor.authorMartinez, Felipe I.
dc.contributor.authorRaveane, Alessandro
dc.contributor.authorCapelli, Cristian
dc.date.accessioned2023-09-01T21:56:28Z
dc.date.available2023-09-01T21:56:28Z
dc.date.issued2023
dc.description.abstractAbstract 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.
dc.fuente.origenORCID
dc.identifier.doi10.1038/s41598-023-40931-x
dc.identifier.urihttp://dx.doi.org/10.1038/s41598-023-40931-x
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/74566
dc.identifier.wosidWOS:001113423900052
dc.information.autorucEscuela de Antropología; Martinez Latrach, Felipe; 0000-0003-0650-4448; 200652
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final12
dc.pagina.inicio1
dc.revistaScientific Reports
dc.rightsacceso abierto
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titleAssessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes
dc.typeartículo
dc.volumenVol. 13
sipa.codpersvinculados200652
sipa.trazabilidadORCID;2023-08-28
Files
Original bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes.pdf
Size:
3.32 MB
Format:
Adobe Portable Document Format
Description: