Isolation, characterization, and marker utility of KCRE1, a transcriptionally active Ty1/copia retrotransposon from Kandelia candel.

Transposable elements are key players in eukaryotic genomic diversity. Due to their high abundance, great heterogeneity, and replicative transposition, long terminal repeat (LTR) retrotransposons are well suited as molecular markers for breeding and biodiversity studies, whereas their utilities in non-model organisms have been hindered by the lack of prior sequence knowledge. In this study, a putative complete (5362 bp) LTR retrotransposon was isolated and characterized in the mangrove species Kandelia candel (named KCRE1), and its transcription, insertional polymorphisms and copy number variations were also investigated. KCRE1 has all the features of a typical copia retroelement, and its transcription initiation and termination sites were identified by 5' and 3' rapid amplification of cDNA ends (RACE), respectively. KCRE1 exhibits high sequence similarity with the tomato retroelement Rider and is constitutively expressed in the leaf, root, flower, and hypocotyl tissues of K. candel. Based on KCRE1, sequence-specific amplification polymorphism (SSAP) markers were developed to explore genetic diversity across 30 individuals from three natural populations of K. candel in China. Six primer combinations yielded a total of 204 SSAP bands with an averaged percentage of polymorphic loci of 55.37 and 41.35 % at the species and population levels, respectively. Each individual had a distinct SSAP phenotype, and 14-23 unique bands were observed for each population. Accordingly, KCRE1 was highly abundant in the genome of K. candel and showed considerable copy number variation among the three populations. In conclusion, KCRE1 is the first transcriptionally active retrotransposon reported in K. candel, providing a useful tool for the elucidation of untapped genetic diversity in mangrove genomes.