Detecting structural variants in the genome of Gallus gallus murghi

Abstract

The Indian Red Junglefowl (Gallus gallus murghi), a key subspecies of the Red Junglefowl and primary ancestor of domesticated chickens, holds immense genetic diversity essential for evolutionary studies. This study analyzed whole genome sequences of ten individuals to characterize their structural variant (SV) landscape using the Manta SV caller. A total of 176,790 SVs were identified, comprising 165,080 insertions, 187,819 deletions, and 2,661 duplications. On average, each genome contained 17,718 insertions, 19,981 deletions, and 266 duplications. Chromosome 1 had the highest SV count (7,296), followed by Chromosomes 2 (5,378) and 3 (4,050). Microchromosomes exhibited the lowest SV counts, with some containing just 1–2 variants. Among sex chromosomes, the Z chromosome had 1,909 SVs, while the W chromosome harbored only 12. Functional annotation revealed significant enrichment in ion channel activity, calcium ion transmembrane transport, and gated channel activity (Molecular Function). Biological Process terms included heart development, regulation of membrane potential, and chondrocyte differentiation. Cellular Component enrichment highlighted ion channel complexes, actin filaments, and the vacuolar membrane. These findings suggest SVs play a vital role in ion transport, skeletal development, and environmental adaptation. This study highlights the structural variability and evolutionary significance of SVs in G. g. murghi. By linking SVs to functional traits, it provides insights into the Red Junglefowl’s adaptability and unique characteristics, offering valuable information for conservation strategies and potential applications in improving poultry breeds.