Chromosomal genomes assemblies of twelve sheep breeds
Abstract
The sheep research community benefits from a genome assembly that has been refined over the last 15 years. However, the rich diversity of sheep breeds suggests that a single individual genome is not enough to represent the species full genomic content. Thirdgeneration sequencing technologies have recently made it possible to generate high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, twelve breeds were selected to represent (mostly French) sheep genetic diversity: Basco-Béarnaise, Black Belly, Blanche du Massif Central, Corse, Ile de France, Lacaune, Manech Tête Noire, Noire du Velay, Ouessant, Rambouillet, Vendéen, Soay. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. The 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 Lacaune 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 11 standard sheep assemblies that pave the way for pangenome construction and structural variant functional studies.
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BibTeX
@misc{camille2026chromosomal,
title = {{Chromosomal genomes assemblies of twelve sheep breeds}},
author = {Eché Camille and Clement Birdes and Camille Marcuzzo and Julien Sarry and Amandine Suin and Caroline Vernette and Claire Kuchly and Christine Gaspin and Denis Milan and Cecile Donnadieu and Carole Iampietro and Gwenola Tosser-Klopp and Christophe Klopp},
howpublished = {HAL},
year = {2026},
month = oct,
doi = {10.64898/2026.10.08.757562},
url = {https://hal.science/hal-05780676v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - UNPB
TI - Chromosomal genomes assemblies of twelve sheep breeds
AU - Eché Camille
AU - Clement Birdes
AU - Camille Marcuzzo
AU - Julien Sarry
AU - Amandine Suin
AU - Caroline Vernette
AU - Claire Kuchly
AU - Christine Gaspin
AU - Denis Milan
AU - Cecile Donnadieu
AU - Carole Iampietro
AU - Gwenola Tosser-Klopp
AU - Christophe Klopp
PY - 2026
DA - 2026/10/06
PB - HAL
DO - 10.64898/2026.10.08.757562
UR - https://hal.science/hal-05780676v1
AB - The sheep research community benefits from a genome assembly that has been refined over the last 15 years. However, the rich diversity of sheep breeds suggests that a single individual genome is not enough to represent the species full genomic content. Thirdgeneration sequencing technologies have recently made it possible to generate high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, twelve breeds were selected to represent (mostly French) sheep genetic diversity: Basco-Béarnaise, Black Belly, Blanche du Massif Central, Corse, Ile de France, Lacaune, Manech Tête Noire, Noire du Velay, Ouessant, Rambouillet, Vendéen, Soay. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. The 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 Lacaune 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 11 standard sheep assemblies that pave the way for pangenome construction and structural variant functional studies.
ER -