Genetic diversity of Ty1-copia retrotransposons in a wild species of Cucumis (C. hystrix)

Ty1-copia retrotransposons are ubiquitous in the plant kingdom and have an important effect on genome structure and evolution. Cucumis hystrix (2n = 2x = 24) is an exotic wild species of Cucumis with a number of valuable traits that are not available in cultivated cucumber. However, lack of the basic genome structure and evolutionary information about C. hystrix has hindered its utilization in cucumber breeding and evolutionary research. In the present study, reverse transcriptase (RT) sequences of Ty1-copia retrotransposons were isolated from genome of C. hystrix by PCR amplification using degenerate oligonucleotide primers. The 24 clones obtained were different from each other and showed high heterogeneity. Of the 24 sequences, 13 are intact whereas the remaining sequences have a stop codon, a frameshift, or both. Southern hybridization revealed that Ty1-copia retrotransposons distributed widely in C. hystrix by multiple copies, and the total number was estimated to be about 5460 as calculated by dot-blot hybridization. The retrotransposons of this kind comprise approximately 8.5% of the C. hystrix genome. No transcription of Ty1-copia retrotransposons was detected by reverse transcriptase PCR (RT-PCR) in leaves of chilling or heat treated plants. Moreover, phylogenetic analysis showed that the 24 RT sequences were divided into five families and had homology with other species, indicating that both vertical transmission and horizontal transmission are the source of Ty1-copia retrotransposons in C. hystrix. FISH with Ty1-copia retrotransposons in C. hystrix revealed the retrotransposons of this kind were widely dispersed over all the chromosomes with clustering in terminal heterochromatin regions. These results contribute to our understanding about the organization and evolution of C. hystrix genome and will provide valuable information for the utilization of retrotransposons in C. hystrix.

Research highlights▶ Reverse transcriptase (RT) sequences of Ty1-copia retrotransposons were isolated from genome of C. hystrix by PCR amplification using degenerate oligonucleotide primers. ▶ Southern hybridization revealed that Ty1-copia retrotransposons distributed widely in C. hystrix by multiple copies. ▶ The total number of Ty1-copia retrotransposons was estimated by dot-blot hybridization. ▶ FISH revealed the retrotransposons of this kind were widely dispersed over all the chromosomes with clustering in terminal heterochromatin regions.