Exploring the genomic landscape of mites and harnessing MITE insertion polymorphism markers in jute (Corchorus sp.)

Jute, a sustainable bast fibre crop from the Malvaceae family, has significant industrial applications and ecological benefits, making it an important focus of recent scientific research. This study investigates the genomic landscape of Miniature Inverted-Repeat Transposable Elements (MITEs), truncated derivatives of autonomous DNA transposons, in two cultivated jute species, Corchorus capsularis and Corchorus olitorius. Genome-wide analysis identified 51,369 and 50,829 MITEs, classified into 632 and 539 families in CC and C. olitorius, respectively. A notable proportion of MITEs were found in genic and near-genic regions, underscoring their potential as tools for gene function exploration. Additionally, 11,801 and 10,921 MITE-derived microRNAs were identified in CC and C. olitorius, emphasizing their roles in genetic and epigenetic regulation. Recognizing the scarcity of molecular markers in jute, this study developed an in-house database of genome-wide MITE insertional polymorphism (MIP) markers. These markers leverage MITEs' unique features-high insertion polymorphism, genic region preference, and short sequence length-making them ideal for molecular breeding. Validation of thirty-eight randomly selected MIP markers across 30 jute accessions demonstrated their efficacy in genetic diversity analysis, grouping the accessions into five distinct clusters. This comprehensive study not only highlights the significance of MITEs in jute genomics but also provides valuable genomic resources for future breeding and improvement programs.