Cloning and analysis of LTR-type retrotransposon RT sequence of Idesia polycarpa Maxim.

Abstract

The present study focuses on the heterogeneity of long terminal repeat (LTR) retrotransposon reverse transcriptase (RT) in Idesia polycarpa Maxim. genome. Using degenerate primers designed by previous scholars, LTR retrotransposon RT sequences of Ty1-copia and Ty3-gypsy, were amplified from the genome of wild I. polycarpa. Cloning and characteristic analysis of these sequences provided insights into the genetic evolution of I. polycarpa genome. Totally, we obtained 92 Ty1-copia-like retrotransposon RT sequences and 43 Ty3-gypsy-like RT sequences of respective lengths 255–269 bp and 431–433 bp. The sequence similarity rates ranged from 27.9 % to 99.2 % and from 52.8 % to 99.5 % for Ty1-copia and Ty3-gypsy RT sequences, respectively. MEGA clustering results showed that Ty1-copia class existed in three original branches of TAR, Ale and Angela, while Ty3-gypsy class exclusively existed in the Tekay original branch. Sequence alignment identified 41 stop codon mutations and 6 frameshift mutations in the Ty1-copia class. The Ty3-gypsy class had 14 termination codon mutations and no frameshift mutation. The ratio of nonsynonymous to synonymous mutations (dN/dS) of LTR retrotransposons in I. polycarpa was below 1, indicating that the Ty1-copia and Ty3-gypsy sequences, despite their significant heterogeneity, undergo purifying selection. Phylogenetic results revealed that theses sequences possess the potential for both horizontal transmission between species and vertical transmission within species.