Next-generation sequencing reveals genomic features in the Japanese quail

Abstract

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.

Third Report on Chicken Genes and Chromosomes 2015

“…Recently, NGS has been used to sequence the genomes of a further 42 avian species, as part of the G10K initiative (Genome 10K Community of Scientists, 2009). In addition there have also been 15 other genome assemblies recently published, each with a focus on a unique aspect of avian biology, including the Japanese Quail (domestication; Kawahara-Miki et al, 2013), Puerto Rican parrot (speciation; Oleksyk et al, 2012), Scarlet Macaw (speech, intelligence and longevity; Seabury et al, 2013), Medium and Large Ground Finches (speciation; Parker et al, 2012; Rands et al, 2013), Collared and Pied flycatchers (speciation; Ellegren et al, 2012), Peregrine and Saker Falcons (predatory lifestyle; Zhan et al, 2013), rock pigeon (domestication; Shapiro et al, 2013), the Ground tit (adaptation to high altitude; Cai et al, 2013) and the Northern Bobwhite (population history; Halley et al, 2014). Through November 2014 there are currently 57 avian genome sequences completed, either published or in press (Table 1).…”

Different Photoperiodic Responses in Four Lines of Japanese Quail

“…The line differences in the testicular regression may originate from all of these tissues and thus their underlying mechanisms remain unknown. Recently, a draft sequence of the quail genome was published, and microsatellite analysis revealed differences in the genetic variability and diversity of quail lines (Kawahara-Miki et al, 2013). Genetic analysis of the four lines of quail augmented by the results from the present study will contribute toward understanding the underlying mechanisms of seasonal testicular regression in future studies.…”

Development and application of genome sequencing in studies on poultry production traits and health

“…On the basis of the draft of the genome sequence comparison, 100 microsatellite markers were developed, which may in the future be used to evaluate the genetic variability of 11 lines of Japanese quail. Based on genomic sequences quail orthologs of spermatogenesis markers were identified (21).…”