Genome-wide characterization of long terminal repeat retrotransposons provides insights into trait evolution of four cucurbit species

• Published in: Functional & integrative genomics 2023-09, Vol.23 (3), p.218-218, Article 218
• Main Authors: Liu, Hai-Nan, Pei, Mao-Song, Ampomah-Dwamena, Charles, He, Guang-Qi, Wei, Tong-Lu, Shi, Qiao-Fang, Yu, Yi-He, Guo, Da-Long
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Cell Biology; Copy number; Crops, Agricultural; Cucurbita; Cucurbita - genetics; Dietary fiber; Genetic diversity; Genomes; Life Sciences; Long terminal repeat; Microbial Genetics and Genomics; Original Article; Phenotype; Phylogenetics; Phylogeny; Plant breeding; Plant Genetics and Genomics; Retroelements - genetics; Single-nucleotide polymorphism; Species; Transposons
• ISSN: 1438-793X; 1438-7948
• DOI: 10.1007/s10142-023-01128-7

Cucurbits are a diverse plant family that includes economically important crops, such as cucumber, watermelon, melon, and pumpkin. Knowledge of the roles that long terminal repeat retrotransposons (LTR-RTs) have played in diversification of cucurbit species is limited; to add to understanding of the roles of LTR-RTs, we assessed their distributions in four cucurbit species. We identified 381, 578, 1086, and 623 intact LTR-RTs in cucumber ( Cucumis sativus L. var. sativus cv. Chinese Long), watermelon ( Citrullus lanatus subsp. vulgaris cv . 97103), melon ( Cucumis melo cv. DHL92), and Cucurbita ( Cucurbita moschata var. Rifu), respectively. Among these LTR-RTs, the Ale clade of the Copia superfamily was the most abundant in all the four cucurbit species. Insertion time and copy number analysis revealed that an LTR-RT burst occurred approximately 2 million years ago in cucumber, watermelon, melon, and Cucurbita , and may have contributed to their genome size variation. Phylogenetic and nucleotide polymorphism analyses suggested that most LTR-RTs were formed after species diversification. Analysis of gene insertions by LTR-RTs revealed that the most frequent insertions were of Ale and Tekay and that genes related to dietary fiber synthesis were the most commonly affected by LTR-RTs in Cucurbita . These results increase our understanding of LTR-RTs and their roles in genome evolution and trait characterization in cucurbits.