EVM_sequence_cds.fa

The freshwater aquaculture species <i>Cirrhinus mrigala</i>, commonly known as mrigal, holds significance in the carp-dominated aquaculture system globally. Despite constituting only 1.08% of the total freshwater aquaculture production, mrigal is the third most important Indian major carp. Thus, this study aims to address this gap by generation high quality genome assembly using PacBio long reads, Illumina short reads, and Hi-C scaffolding. The characterization of assembled highly contiguous genome, 1.057 Gb in size, includes repeats characterization and gene prediction, revealed 22,181 unique genes with functional annotations. The orthology analysis based on genes with single copy places <i>C. mrigala</i> in a distinct position within the Otophysi clade. Additionally, the study delves into Hox gene clusters, identifying 38 Hox genes distributed in seven clusters. The present genomic information offers potential applications for sustainable aquaculture management, including selection programs for economic traits.