Genome-wide characterization of LTR retrotransposons provides new insights into missed gene annotation and gene expression effects in pear genomes

Abstract Long terminal repeat retrotransposons (LTR-RTs) are crucial genomic elements that play a key role in shaping plant genome evolution and diversity. With the availability of high-quality genome sequences, an unprecedented opportunity has emerged to investigate LTR-RT dynamics in depth. This study presents a thorough analysis of LTR-RTs across six pear genomes. By integrating structure-based and homology-based approaches, this study identified 36,552 LTR-RTs, which included 18,302 complete LTR-RTs (50.07%), 13,793 solo LTRs (37.74%), 2,304 truncated LTR-RTs (6.30%), and 1,104 fragmented LTR-RTs (3.02%). These elements were classified into 1,075 distinct families, spanning four superfamilies: Copia (43 ± 6%), Gypsy (34 ± 7%), terminal repeat retrotransposons in miniature (TRIM) (13 ± 7%), and large retrotransposon derivatives (LARD) (10 ± 5%). The majority of LTR-RTs (64.16%) were inserted recently (0–0.5 Mya), with younger elements generally exhibiting higher copy numbers. Mapping results showed that 91.3% of complete LTR-RTs were successfully mapped to 17 chromosomes and were positively correlated with chromosome size ( r = 0.851–0.976, P < 0.01). A total of 5,332 intact LTR-RTs (36.16%) were collinear across all six genomes, indicating insertions prior to species divergence. Over half of the LTR-RTs (54.65%) were located within genes or their flanking regions, with a strong preference for upstream (48.52%) and downstream (43.19%) regions over intragenic locations (6.37%). LTR-RT insertions significantly influenced gene expression in a manner specific to each variety. Furthermore, 5,217 previously unannotated genes interrupted by LTR-RTs were identified, of which 78.95% were functional, and 75% displayed active expression. This study provides comprehensive insights into the evolutionary dynamics and functional impact of LTR-RTs in pear genomes, enhancing our understanding of genome evolution and regulation in fruit crops.