Hi-C guided genome assembly and karyotype analysis of the Indian population of Maruca vitrata (Lepidoptera: Crambidae) set the stage for structural and functional genomic insights

The spotted or legume pod borer, Maruca vitrata (Lepidoptera: Crambidae), is a global insect pest of many economically important grain and vegetable legume crops. Although the species is believed to have originated in the Indo-Malayan region, populations in India have shown evidence of genetic divergence, potentially representing distinct cryptic species or host-associated races. A comprehensive understanding of the evolutionary relationships and functional divergence within M. vitrata is currently limited by the absence of detailed genomic resources. Integrating karyotype data with high-resolution genomic information is therefore essential to elucidate the genetic architecture and evolutionary dynamics of the Indian lineage of M. vitrata and to inform effective pest management strategies.

PacBio HiFi sequencing and proximity ligation technique (Hi-C), we provide here an improved genome assembly of M. vitrata. The 459.3 Mb genome was assembled into 45 scaffolds with a scaffold N50 of 15.6 Mb. The 31 pseudochromosomes (size range from 9.48 to 20.42 Mb) accounted for 458 Mb, representing 99.73% of the genome assembly. The genome has a repeat content of 36.67% and 21,586 protein-coding genes. The genome completeness analysis using BUSCO with the Insecta lineage((Insecta_odb10) captured 99.5% of the complete BUSCOs. The karyotype analysis revealed the presence of 31 chromosomes (1n). This genome-scale data helps by identifying target genes for the development pest management strategies in the future. The 31 pseudochromosomes correspond to the 31 chromosomes identified through karyotype analysis, thereby confirming the chromosomal-level completeness and structural accuracy of the assembly.