Landscape of transposable element polymorphism across geographically diverse samples of the grasshopper Trilophidia annulata

Transposable elements (TEs), often referred to as “jumping genes”, constitute a major fraction of eukaryotic genomes. TE polymorphism is increasingly recognized as an important source of genomic variation underlying geographic divergence and local adaptation. Orthoptera is the only insect lineage known to have undergone pronounced genome gigantism, largely driven by TE expansion. We investigated TE polymorphism in the grasshopper Trilophidia annulata (genome size 9.94 Gb) using short-read genome sequencing data from four individuals sampled at geographically distinct locations in China (Xi’an, Yan’an, Kunming, and Dali). For each individual, the sequencing data were independently subsampled four times. Across these individuals, TE genomic proportions ranged from 62.41 ± 0.09% to 63.02 ± 0.15%. However, the number of annotated TE consensus sequences ranged from 24,950 ± 60.7 in Xi’an to 31,003 ± 187.3 in Dali. Approximately 30% (7,700–8,700) of annotated TE consensus sequences had more than 10 copies, while pairwise comparisons revealed that approximately half of the TE consensus sequences were individual-specific. These individual-specific TEs generally occurred at low copy numbers, whereas shared TEs dominated overall TE content. Accumulation pattern analyses further indicated that shared TEs exhibit conserved profiles across the four geographically disparate individuals, although some sample-specific clustering patterns were observed in phylogenetic analyses of LTR reverse transcriptase domains. Our results demonstrate that the genomic repeat landscape of T. annulata is conserved among individuals from different geographic locations. Shared TEs contribute substantially to overall TE content, whereas differences among individuals are characterized by copy number variation and sequence diversification rather than large-scale amplification. These findings provide insights into TE dynamics during geographic divergence and provide a baseline for future population-level tests of adaptation.