Year: 2026
Type: preprint
Abstract: A bstract The goat research community benefits from one of the most comprehensive livestock genome assemblies, ARS1. However, the rich diversity of goat breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate very high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, nine goat breeds were selected to represent French goat genetic diversity: Alpine, Boer, Créole, Fossés, Poitevine, Provençale, Pyrénéenne, Rove and Saanen. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. There reads were used to generate de novo assemblies and were aligned onto the public reference to call structural variants. PacBio HiFi and parental Illumina reads were used to assemble phased haplotypes of the Alpine breed. For the other breeds, PacBio raw (CLR) or ONT reads were generated. Our work demonstrates the feasibility of assembling genomes with a reasonable amount of data and appropriate software packages, delivering one high-quality assembly and 8 standard goat assemblies that pave the way for pangenome construction and structural variant functional studies.
Institutions: Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Genotoul coordination, Génome et Transcriptome - Plateforme Génomique, École Nationale Vétérinaire de Toulouse, Institut National Polytechnique de Toulouse, Génétique Physiologie et Systèmes d'Elevage, AgroParisTech, Université Paris-Saclay, Génétique Animale et Biologie Intégrative, Mathématiques et Informatique Appliquées Toulouse
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W7221435624