Isolation, identification and characterization of Jute Genomic LTR retrotransposon sequences

Abstract

Long Terminal Repeat (LTR) retrotransposons make up a significant part of eukaryotic genomes and play an important role in plant genome evolution. Jute is an important fiber crop, and the Jute genome, consisting of 1,250 Mbps, is largely unexplored. In this study an attempt was made to identify and characterize the LTR retrotransposons of the Jute genome Chorchoru solitorius in order to understand the genome better. The Reverse Trancriptase domain of Ty l -copia and Ty3-gypsy LTR retrotransposons of Jute were amplified by degenerate primers. The sequences were analyzed and clustered into groups. Reverse transcriptase PCR was used to analyze any transcriptional activity. Sequence analysis showed a higher heterogeneity among Tyl-copia retrotransposons than Ty3-gypsy retrotransposons. One of the groups of retrotransposon Tyl-copia was found to be transcriptionally active. As the LTR retrotransposons constitute a large portion of the Jute genome, the findings of this study suggest the importance of these elements in Jute genome evolution.