Abstract
Japanese quail (Coturnix japonica) is an important poultry species selectively bred for its egg and meat production. India ranks third amongst the top five quail meat producing countries in the world. Considering the convoluted history of domestic C. japonica lines development worldwide, no genome scale information is available on commercially available C. japonica lines in India. Hence, we generated whole genome sequences from a commercially available C. japonica specimen and mined genome-wide microsatellites from the same. A total of 130,336,082 paired-end reads with an estimated coverage of ~ 20× was sequenced. The sequenced data displayed optimal Kmer value of 53, 90.6% unique reads, 0.648% heterozygosity and 0.17% duplication rate. The reads were assembled De-novo into 134,191 contigs spanning a genome length of 0.92 Gb, GC content of 41.08% and contig N50 value of 23.35 Kbp. BUSCO analysis revealed the presence of 88.3% of all orthologous avian gene sets being identified in the generated assembly. A total of 287,741 microsatellite motifs were identified from the C. japonica SPAdes assembly sequenced in this study covering 0.62% of the total genome length. Dinucleotide constituted the highest number of motif types and repeats of AA, AC, AG, AT, CC, CG, AAC, AAG, AAT and ACC were identified as the most abundant repeats types. The C. japonica genome and SSR markers identified in this study will be helpful in future evolutionary and population genetics studies on quails. The SSR markers will also serve as important tool for forensic studies.
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All the sequence generated and utilized in this study are associated in the Accession numbers: BioProject, BioSample and SRA numbers are PRJNA840867, SAMN28561720 and SRR19344531.
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This work was supported and funded by Ministry of Environment, Forests and Climate Change, Government of India.
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Dey, P., Ray, S.D., Manchi, S. et al. Whole genome sequencing and microsatellite motif discovery of farmed Japanese quail (Coturnix japonica): a first record from India. Proc.Indian Natl. Sci. Acad. 88, 688–695 (2022). https://doi.org/10.1007/s43538-022-00118-w
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DOI: https://doi.org/10.1007/s43538-022-00118-w