Heterogeneous evolution of Ty3-gypsy retroelements among bamboo species

Ty3-gypsy long-terminal repeat retroelements are ubiquitously found in many plant genomes. This study reports the occurrence of heterogeneous Ty3-gypsy retroelements in four representative bamboo species: Phyllostachys heterocycla (Carr.) Mitford cv. pubescens, P. heterocycla (Carr.) Mitford cv. heterocycla, Dendrocalamopsis oldhami, and Pleioblastus fortunei. Using degenerate oligonucleotide primers corresponding to the conserved domains of reverse transcriptase (rt) genes of Ty3-gypsy retroelements, 165 distinct sequences were amplified from genomic DNA. The length of the nucleotide sequences varied from 366 to 438 bp. The sequences demonstrated a high heterogeneity, with homology ranging from 52.2 to 99.8%. A phylogenetic tree was constructed, including Arabidopsis thaliana and Oryza sativa. Bamboo Ty3-gypsy sequences formed three distinct retroelement clusters (gypsy I-III). Further analysis indicated that there were not only nearly identical Ty3-gypsy retroelements found in distantly related species, but also highly diverse Ty3-gypsy retroelements observed in closely related species. The results of this study provide genetic and evolutionary information about the bamboo genome that could contribute to further studies of repetitive elements in bamboo as well as in other species.