Isolation and Analysis of Reverse Transcriptase of Ty1-copia-Like Retrotransposons in Sugarcane

In this study, the reverse transcriptase sequences of Ty1-copia-like retrotransposons were amplified from ROC22 and Badila, and their characteristics, diversity, phylogenetic relationships and transcriptional activity were analyzed. The genomic DNA was amplified by PCR using degenerate primers. The targeted amplified bands in both varieties are all about 260 bp in size. Forty-four and thirty-eight sequences were isolated from ROC22 and Badila, respectively. The length of the former and the latter ranged from 233 to 263 bp and from 233 to 264 bp. The proportion of AT content in the former and in the latter ranged from 45.63 to 62.74% and from 50.58 to 65.40%. The ratio of AT to GC in the former and in the latter ranged from 0.84 to 1.68 and from 1.02 to 1.89. The similarity between nucleotide sequences in the former and in the latter ranged from 47.9 to 98.5% and from 42.3 to 98.8%. According to the cluster analysis, the former was divided into two families, of which family I was divided into five subfamilies. The latter was also divided into two families, of which family I was divided into six subfamilies and family II was divided into three subfamilies. Six of the former and fourteen of the latter had nonsense mutations. The nonsense mutations rate of the latter was much higher than that of the former. The similarity between amino acids in the former and in the latter ranged from 12.9 to 100% and from 42.3 to 98.8%, and the heterogeneity of the latter was lower than that of the former. There were differences in the length of main conserved motifs between the two varieties. The differences of protein structure in the Badila were greater than in the ROC22, and the structure of sequences in the Badila was more complex. The phylogenetic tree showed that all sugarcane reverse transcriptase sequences were divided into six classes. It was found that eleven sugarcane Ty1-copia-like retrotransposons had transcriptional activity. And the transcriptional activity of Ty1-copia-like retrotransposons in the ROC22 was higher than that of Ty1-copia-like retrotransposons in the Badila. The obtained sequences will provide sequences basis for isolating the full-length sequences of Ty1-copia-like retrotransposons, studying their transcriptional transposition activity and function, and laying the foundation for the development of molecular markers in sugarcane.

Automated summary

This study analyzed the characteristics, diversity, phylogenetic relationships, and transcriptional activity of Ty1-copia-like retrotransposons in ROC22 and Badila. The results showed differences in length, AT content, and nucleotide similarity between the two varieties. The research on sugarcane reverse transcriptase sequences is of great importance.