Whole genome sequencing and microsatellite motif discovery of farmed Japanese quail (Coturnix japonica): a first record from India

Dey, Prateek; Ray, Swapna Devi; Manchi, Shirish; Pramod, Padmanabhan; Kochiganti, Venkata Hanumat Sastry; Singh, Ram Pratap

doi:10.1007/s43538-022-00118-w

Cited by 2 publications

(3 citation statements)

References 30 publications

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“…For C. japonica , a commercially farmed specimen from India was sampled from the market, and the biomaterials (muscle tissue and blood) were stored in DESS buffer and transported to the lab under suitable conditions as stated above. The specifics of the C. japonica sample and the whole genome sequences produced are detailed in a prior publication by our research group [ 14 ]. To construct the C. japonica mitochondrial genome, we utilized the raw sequencing reads as reported in [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

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Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails

Dey,

Ray,

Kochiganti

et al. 2024

Genes

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The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau’s geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.

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Section: Methodsmentioning

confidence: 99%

“…The specifics of the C. japonica sample and the whole genome sequences produced are detailed in a prior publication by our research group [ 14 ]. To construct the C. japonica mitochondrial genome, we utilized the raw sequencing reads as reported in [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails

Dey,

Ray,

Kochiganti

et al. 2024

Genes

Self Cite

View full text Add to dashboard Cite

show abstract

“…Subsequently TruSeq DNA PCR-Free library preparation kit was used to clean-up the fragmented DNA, create blunt-ends and ligate adapters to the library fragments performed. Previous works outline the detail methodology for library preparation [ 6 , 7 ]. Upon successful library preparation mean peak size of the pair-end library created was assessed using Fragment Analyzer AATI 5200 (Agilent, USA) and quantified using QIAseq Library Quant Assay Kit (Qiagen N.V., Germany).…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Dataset from genome sequencing, assembly and mining of microsatellite markers in barred-button quail (Turnix suscitator)

et al. 2023

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Whole genome sequencing and microsatellite motif discovery of farmed Japanese quail (Coturnix japonica): a first record from India

Cited by 2 publications

References 30 publications

Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails

Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails

Dataset from genome sequencing, assembly and mining of microsatellite markers in barred-button quail (Turnix suscitator)

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