DKRE1—The first full-length Ty1-copia-like retrotransposon in persimmon: Isolation, characteristic and potential involvement in occurrence of bud mutations

Abstract

The focus of this study revolved around persimmon (Diospyros kaki Thunb.) retrotransposable element 1 (DKRE1), a complete long terminal repeat (LTR) retrotransposon (RTN) that was isolated from persimmons. Its structure, phylogenetic classification, copy number, active characteristics and potential roles involved in the occurrence of bud mutations in persimmons were investigated. Having a length of 6, 235bp, DKRE1 possessed all of the sequence features associated with Ty1-copia-like retrotransposons. Phylogenetic analysis showed significant, but not strong, identity in amino acid sequences with BARE1 (barley retrotransposable element-1), RIRE1 (rice retrotransposable element-1) and Ppcrt (Pyrus pyrifolia copia retrotransposon) groups. The estimated copy number of 45 copies per haploid genome suggested that DKRE1 possesses a low constitution in the persimmon genome. Furthermore, the transcription of DKRE1 could be detected in leaf tissue treated with salicylic acid (SA), methyl jasmonate (MJA), and abscisic acid (ABA), indicating its active characteristics when subjected to exogenous phytohormones. Polymorphisms were revealed between several pairs of bud mutations by way of either inter-retrotransposon amplified polymorphism (IRAP) or sequence-specific amplified polymorphism (SSAP) retrotransposon-based molecular markers, showing a potential involvement in their occurrence. To our knowledge, this is the first report of the isolation of a complete LTR retrotransposon with transcriptional activity in persimmons. This study is valuable for future research on the mechanisms of bud mutation and development of retrotransposon-based molecular markers for genetic analysis.