【Coturnix japonica】

The Japanese quail (Coturnix japonica, Phasianidae, Galliformes), also known as Coturnix quail, is a species of Old World quail found in East Asia. First considered a subspecies of the Common quail, it was distinguished as its own species in 1983. The Japanese quail and chicken are estimated to have diverged 35 million years ago (MYA) by molecular phylogenetic analysis (van Tuinen et al. 2004). The Japanese quail has played an active role in the lives of humanity since the 12th century, and continues to play major roles in industry and scientific research. This migratory bird, with small body size (100~300 g), short generation interval, and high resistance to disease, is an excellent model animal for a wide range of scientific research. In addition, this species is economically important as an egg- and meat-producing agricultural animal that is reared in many countries worldwide. Although the Japanese quail has several advantages as a laboratory animal for biological and biomedical investigations and as a pilot animal for poultry science, the development of quail genome information has been still insufficient. This prevents the practical use of this animal species. We here open the genome browser of the Japanese quail as a web-based tool, which is built using our most recently updated data of the quail genome assembly.

【Karyotype】

The diploid number of chromosomes is 78 in both the chicken and Japanese quail (Sasaki 1981). Comparative gene mapping of cDNA and genomic DNA clones using fluorescence in situ hybridization (FISH) revealed that the genetic linkage groups are highly conserved between the chicken and quail; however, the Japanese quail differed from the chicken in chromosomes 1, 2, and 8 by pericentric inversion and in chromosome 4 by centromere repositioning (Shibusawa et al. 2001).

【Resource】

The NIES-L quail strain was used for whole genome sequencing. This strain has been maintained for more than 70 generations by rotation breeding system as a closed colony. NIES-L was established as a low responder strain in antibody-production to inactivated Newcastle disease virus vaccine, and is fixed in one major histocompatibility complex (MHC) haplotype. This strain has been used widely for reproductive and developmental toxicity testing of endocrine disrupting chemicals. NIES-L was derived from National Institute of Environmental Studies, Tsukuba, Japan, and is maintained at Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, under the support of the National Bio-Resource Project of the Ministry of Education, Culture, Sports, Science and Technology, Japan.

【Genome sequence information】

Whole-genome sequencing of the NIES-L strain was performed using a total of 15 libraries, 10 pair-end libraries, and five mate-pair libraries on HiSeq 2000 and GAII sequencers (Illumina, San Diego, CA) at NODAI Genome Research Center, Tokyo University of Agriculture, Japan (Kawahara-Miki et al. 2013; Ishishita et al. in preparation). In the first version of the genome assembly released on January 29, 2016, total assembled sequence coverage was 248-fold coverage of the Japanese quail genome, and the estimated genome size was 0.94 Gb. A total of 192 Gbp of paired-end reads and 40 Gbp of mate-pair reads were assembled, yielding 9,499 scaffolds and 65,900 large contigs (>1,000 bp). The N50 scaffold length was 3,851,064 bp, and the N50 contig length was 30,310 bp. This assembly spaned 898 Mb.

We updated the assembled genome sequence data by adding 688.5 million reads using 10X Genomics Chromium system and 1.7 million reads using PacBio Sequel system on September 26, 2019. The total assembled sequence coverage in the second version have increased to 376-fold coverage, and the estimated genome size is 1.0 Gb. Assembling of total reads have yielded 2,538 scaffolds and 21,892 large contigs (>1,000 bp). The N50 scaffold length is 81,982,712 bp, and the N50 contig length is 174,303 bp. The assembly spans 932 Mb.

【Contribution】

Whole genome sequencing was performed by Ryoka Kawahara-Miki and Tomohiro Kono, Tokyo University of Agriculture; a high-quality chromosome-scale assembly of the genome was generated by Shoji Tatsumoto and Yasuhiro Go, Center for Novel Science Initiatives, National Institute of Natural Sciences; the genome viewer was built by Yohei Minakuchi and Yukiko Yamazaki, National Institute of Genetics. Matsuda Y played a role in coordinating the Quail Genome Consortium of Japan.

【Members of the consortium】

Tomohiro Kono,
Department of Bioscience, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan

Ryoka Kawahara-Miki,
NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan

Yasuhiro Go, Shoji Tatsumoto,
Department of Brain Sciences, Center for Novel Science Initiatives, National Institute of Natural Sciences, Okazaki, Aichi 444-8585, Japan

Shuji Shigenobu, Katsushi Yamaguchi,
NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan

Yukiko Yamazaki, Shoko Kawamoto,
Genetic Informatics Laboratory, Research Organization of Information and Systems,
National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan

Yoichi Matsuda,
Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan

【References】

Kawahara-Miki R, Sano S, Nunome M, Shimmura T, Kuwayama T, Takahashi S, Kawashima T, Matsuda Y, Yoshimura T, Kono T. Next-generation sequencing reveals genomic features in the Japanese quail. Genomics 101, 345–353, 2013.

Sasaki M. High resolution G-band karyotypes of thedomestic fowl and the Japanese quail. Chrom Inform Sevice 31: 26–28, 1981.

Shibusawa M, Minai S, Nishida-Umehara C, Suzuki T, Mano T, Yamada K, Namikawa T, Matsuda Y. A comparative cytogenetic study of chromosome homology between chicken and Japanese quail. Cytogenet Cell Genet 95: 103–109, 2001.

van Tuinen M and Dyke GJ. Calibration of galliform molecular clocks using multiple fossils and genetic partitions. Mol Phylogenet. Evol 30: 74–86, 2004.