VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Authors: DENOYELLE, LAURE - Collaborator; TALOUARN, ESTELLE - Collaborator; BARDOU, PHILIPPE - Collaborator; COLLI, LICIA - Università Cattolica Del Sacro Cuore; ALBERTI, ADRIANA - Collaborator; DANCHIN, CORALINE - Collaborator; DEL CORVO, MARCELLO - Università Cattolica Del Sacro Cuore; ENGELEN, STEFAN - Collaborator; ORVAIN, CELINE - Collaborator; PALHIERE, ISABELLE - Collaborator; RUPP, RACHEL - Collaborator; SARRY, JULIEN - Collaborator; SALAVATI, MAZDAK - Roslin Institute; AMILLS, MARCEL - Autonomous University Of Barcelona; CLARK, EMELY - Roslin Institute; CREPALDI, PAULA - Autonomous University Of Barcelona; FARAUT, THOMAS - Collaborator; MASIGA, CLET WINDUI - Tropical Institute Of Development Innovation (TRIDI); PAMPANON, FRANÇOIS - Universite Grenoble Alpes; Rosen, Benjamin - Ben; STELLA, ALESSANDRA - Consiglio Nazionale Delle Ricerche; Van Tassell, Curtis - Curt; TOSSER-KLOPP, GWENOLA - Collaborator; VARGOATS CONSORTIUM - Collaborator

Submitted to: Genetic Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/22/2021
Publication Date: 11/8/2021
Citation: Denoyelle, L., Talouarn, E., Bardou, P., Colli, L., Alberti, A., Danchin, C., Del Corvo, M., Engelen, S., Orvain, C., Palhiere, I., Rupp, R., Sarry, J., Salavati, M., Amills, M., Clark, E., Crepaldi, P., Faraut, T., Masiga, C., Pampanon, F., Rosen, B.D., Stella, A., Van Tassell, C.P., Tosser-Klopp, G., The Vargoats Consortium. 2021. VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity. Genetic Selection Evolution. 53:86. https://doi.org/10.1186/s12711-021-00659-6.
DOI: https://doi.org/10.1186/s12711-021-00659-6

Interpretive Summary: The VarGoats project is an international collaboration. The goal of this group is to sequence at least 1,000 genomes to better understand the consequences of domestication and selective breeding on the genetic diversity of domestic goats. An additional goal is to understand the process of spcies formation and crossing have affected the genomes of a set of species representative of the genus Capra (goats). We have built the VarGoats dataset by sequencing the genomes of 652 goats with a worldwide distribution as well as by retrieving 508 goat genome sequences from public databases. These public data include 35 animals from 8 wild goat species. Comparisons of these sequences revealed over 74 million single base changes and over 13 milllion small genomic insertions and deletions. Analysis of these genetic variants has demonstrated that goats from Africa, Asia and Europe tend to group in independent continental clusters. This wide panel of sequenced individuals represents an unprecedented opportunity to determine how the formation of species and breeds and selective breeding have shaped the diversity of this species.

Technical Abstract: The VarGoats project is an international 1,000 genomes resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats, as well as to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. We have built the VarGoats dataset by sequencing the genomes of 652 goats with a worldwide distribution as well as by retrieving 508 goat sequences from public databases, including 35 animals from 8 wild goat species. Alignment of these sequences revealed 74,274,427 SNPs and 13,607,850 INDELs. Performance of a phylogenetic analysis has demonstrated that goats from Africa, Asia and Europe tend to group in independent continental clusters. This wide panel of sequenced individuals represents an unprecedented opportunity to ascertain how the demographic and selection processes associated with domestication and breeding have shaped the diversity of this species.