New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)
Abstract
The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.
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BibTeX
@misc{cabau2026chromosomelevel,
title = {{New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)}},
author = {Cédric Cabau and Fabien Degalez and Sophie Leroux and David Gourichon and Rémy-Felix Serre and Caroline Vernette and Cécile Donnadieu and Carole Iampietro and Céline Vandecasteele and Frédérique Pitel and Christophe Klopp},
howpublished = {HAL},
year = {2026},
month = may,
doi = {10.64898/2026.05.12.724545},
url = {https://hal.inrae.fr/hal-05786765v1},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - UNPB
TI - New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)
AU - Cédric Cabau
AU - Fabien Degalez
AU - Sophie Leroux
AU - David Gourichon
AU - Rémy-Felix Serre
AU - Caroline Vernette
AU - Cécile Donnadieu
AU - Carole Iampietro
AU - Céline Vandecasteele
AU - Frédérique Pitel
AU - Christophe Klopp
PY - 2026
DA - 2026/05/14
PB - HAL
DO - 10.64898/2026.05.12.724545
UR - https://hal.inrae.fr/hal-05786765v1
AB - The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.
ER -