Next-generation sequencing reveals genomic features in the Japanese quail

• We assembled the draft genome of Japanese quail using next-generation sequencing.
• We developed 100 novel microsatellite markers for the Japanese quail.
• Markers were applied to evaluate the genetic background of 11 Japanese quail lines.
• We have identified Japanese quail orthologs of spermatogenesis markers.
• Obtained genome sequence could enhance the value of this species as a model animal.

The Japanese quail has several advantages as a laboratory animal for biological and biomedical investigations. In this study, the draft genome of the Japanese quail was sequenced and assembled using next-generation sequencing technology. To improve the quality of the assembly, the sequence reads from the Japanese quail were aligned against the reference genome of the chicken. The final draft assembly consisted of 1.75 Gbp with an N50 contig length of 11,409 bp. On the basis of the draft genome sequence obtained, we developed 100 microsatellite markers and used these markers to evaluate the genetic variability and diversity of 11 lines of Japanese quail. Furthermore, we identified Japanese quail orthologs of spermatogenesis markers and analyzed their expression using in situ hybridization. The Japanese quail genome sequence obtained in the present study could enhance the value of this species as a model animal.