Transposable element evolution, infection responses, and resistance-linked insertions in the shrimp Litopenaeus vannamei

Intrinsic genetic and expression variation shapes economically important and disease-resistance traits, and transposable elements (TEs) may contribute through their genomic abundance and regulatory potential. However, TE landscapes, infection-responsive dynamics, and insertion polymorphisms (TIPs) remain poorly defined in shrimp. Here, we analyzed five shrimp genomes and profiled TE expression in Litopenaeus vannamei gills during infection with Vibrio parahaemolyticus (Vpa), white spot syndrome virus (WSSV), and decapod iridescent virus 1 (DIV1), and identified resistance-associated TIPs using bulk-segregant analysis sequencing (BSA-seq). The L. vannamei TE landscape is dominated by LINE/CR1 and PLE/Penelope, with an expansion of RC/Helitron but few intact LTR/Gypsy elements. Across infections, TE expression was predominantly repressed, and responsive elements showed family-level biases. Differentially expressed TEs were generally longer and more GC-rich, and were dominated by in LINE/CR1 and LTR/Gypsy families. Genes near responsive TEs were enriched for innate immune functions and for metabolic and growth pathways. Across stimuli, 109 TEs responded (89 downregulated and 20 upregulated), with LTR retrotransposons overrepresented among upregulated elements and DNA transposons and RC/Helitron among downregulated elements. We identified 18 TE–gene pairs with concordant changes, with most insertions in promoters, introns, or exons. BSA-seq detected 27 high-confidence TIPs, mainly intergenic and dominated by LTR/Gypsy, including variants enriched in susceptible or resistant pools. Together, these results define stimulus-dependent TE regulation in shrimp and support regulatory links between TEs and pathogen defense. • Litopenaeus vannamei TEs are dominated by LINE/CR1 and PLE/Penelope. • TE responses to Vpa, WSSV, and DIV1 are broadly repressive in L. vannamei . • TE-gene proximity within ±10 kb links TEs to innate immune pathways. • Co-regulated TE-gene pairs include CYP450s and a mite allergen-like gene. • Bulked-segregant mapping yields 27 TIPs, enriched in intergenic LTR/Gypsy.