Genome-wide detection of Ty1-copia and Ty3-gypsy group retrotransposons in Japanese apricot (Prunus mume Sieb. et Zucc.)

Abstract

The conserved domains of reverse transcriptase (RT) genes of approximately 260 bp for Ty1-copia and 430 bp for Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were amplified from
Japanese apricot (Prunus mume Sieb. et Zucc.) using degenerate oligonucleotide primers. Sequence analysis showed that 32.3% of Ty1-copia and 27.5% of Ty3-gypsy RT sequences possessed stop codons and/or frameshifts, and all sequences were AT-rich. Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon, but the latter has a higher copy number revealed by
southern dot blot hybridization. Phylogenetic analysis illustrated that some of the clones were more closely related to the representative elements present in other plant species than to other clones of Japanese apricot. Transcription was not detected by reverse transcription-polymerase chain reaction amplification for either Ty1-copia or Ty3-gypsy retrotransposons in young leaves of plants treated with UV light and 2,4-dichlorophenoxyacetic acid either individually or in both combinations, even though the ratios of dN/dS of the open reading frames among members of each subgroup of both group retrotransposons were less than 1. This is the first report on the presence of RT sequences of Ty1-copia and Ty3-gypsy group retrotransposons in Japanese apricot genome.

Keywords: Prunus mume, retrotransposon, heterogeneity, copy number, transcriptional activity