What's new

  • 2016.01.29

    "Japanese Quail (Coturnix japonica) Genome Sequencing Project" website was released.

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 35million 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 its 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 has been built using our most recently updated data of the quail genome assembly.
Karyotype】【Resource】【Genome sequence information】 【Contribution】 【Members of consortium】 【References

Summary of sequence data used to assemble the quail genome.
Library (insert size) # of libraries Read length (bp) Raw Filter Sequencing Platforms
Number of reads (million) Number of bases (giga) Coverage (x) Number of reads (million) Number of bases (giga) Coverage (x)
Pair-end (300 bp)210097.49.710.491.28.49.0Illumina HiSeq 2000
Pair-end (500 bp)210060.46.06.458.65.55.9Illumina HiSeq 2000
Pair-end (300 bp)1101223.922.624.1206.219.520.8Illumina HiSeq 2000
Pair-end (500 bp)1101221.422.423.8202.219.220.5Illumina HiSeq 2000
Pair-end (300 bp)1102136.313.914.8124.411.712.5Illumina HiSeq 2000
Pair-end (500 bp)1102193.719.821.1178.716.918.1Illumina HiSeq 2000
Pair-end PCR-free (300 bp)1100865.386.592.3809.773.177.9Illumina HiSeq 2000
Pair-end PCR-free (500 bp)1100538.353.857.4473.238.140.6Illumina HiSeq 2000
Mate-pair (3 kbp)236101.23.63.990.83.33.5Illumina GAII
Mate-pair (5 kbp)23645.41.61.728.61.01.1Illumina GAII
Mate-pair (10 kbp)1100408.440.843.6385.735.738.1Illumina HiSeq 2000
10X Genomics linked-reads1100688.5103.3110.8688.5103.3110.8Illumina HiSeq X Ten
PacBio18,944*1.714.815.91.714.815.9PacBio Sequel
*average length
Japanese quail assembly statistics.
Assembly # of contigs (w/o gaps) N50 (contig) # of gaps total gap length # of scaffolds N50 (scaffold) total length
10X Chromium Genome linked-reads + PacBio reads34,366161,33423,53943,071,64110,82320,385,050999,596,594
With added information from alignments against galGal521,892174,30319,35536,492,5372,53881,982,712932,102,785
First version (all)305,50728,46157,68217,858,319247,8253,678,261937,605,096
First version (>1k)65,90030,31056,40117,810,0129,4993,851,064898,141,602