Goat genome assemblies, nine breeds for pangenome contribution
Abstract
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.
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BibTeX
@misc{birdes2026goat,
title = {{Goat genome assemblies, nine breeds for pangenome contribution}},
author = {Clement Birdes and Eché Camille and Caroline Vernette and Camille Marcuzzo and Julien Sarry and Amandine Suin and Claire Kuchly and Odile Rogier and Christine Gaspin and Denis Milan and Cécile Donnadieu and Carole Iampietro and Christophe Klopp and Gwenola Tosser-Klopp},
howpublished = {Peer Community Journal},
year = {2026},
month = oct,
doi = {10.64898/2026.10.08.757565},
url = {https://hal.science/hal-05780938v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - UNPB
TI - Goat genome assemblies, nine breeds for pangenome contribution
AU - Clement Birdes
AU - Eché Camille
AU - Caroline Vernette
AU - Camille Marcuzzo
AU - Julien Sarry
AU - Amandine Suin
AU - Claire Kuchly
AU - Odile Rogier
AU - Christine Gaspin
AU - Denis Milan
AU - Cécile Donnadieu
AU - Carole Iampietro
AU - Christophe Klopp
AU - Gwenola Tosser-Klopp
PY - 2026
DA - 2026/10/06
PB - Peer Community Journal
DO - 10.64898/2026.10.08.757565
UR - https://hal.science/hal-05780938v1
AB - 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.
SN - 2804-3871
SN - 2804-3871
ER -