KadakExpress — a tissue-specific gene expression atlas of the Indian black chicken breed

Kadaknath is the only black meat native Indian chicken breed with great economic value. However, the dearth of genomic information limits the possibility of undertaking its selective breeding, sustainable production, and conservation. Here we present a comprehensive database of Kadaknath chicken gene expression namely KadakExpress that provides an insight into the genomic biology and function of various genes expressed across 16 major tissues. RNA sequencing-based transcriptomics was used to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary Kadaknath tissues, and present supplementary analyses. The quality of raw and trimmed reads was assessed in terms of base quality, GC content, duplication sequence rate, overrepresented k-mers, and quality score distribution with FastQC. The database consists of 39,679 genes, 3,83,176 gene-to-GO annotation associations (comprising Biological Process, Molecular Function, and Cellular Component categories) and 5,727 Reactome database pathway annotations. The maximum number of unique genes was identified in the brain (302) while 1608 unique genes were detected across 16 tissues. Further, search options were designed to retrieve the desired information efficiently. This multi-tissue transcriptomic database of Indian black chicken has been made available to the scientific community and would serve as a valuable resource for the identification and analysis of genes, pathways, and networks in chickens. KadakExpress provides a comprehensive transcriptomic resource that facilitates future investigations into the molecular basis of black meat pigmentation, disease resistance, environmental adaptation, and other economically important traits in Kadaknath chicken.