An M M, Guo C, Lin P P, Zhou M B
The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Department of Silviculture, Zhejiang A&F University, Lin'an, Zhejiang, China.
The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Department of Silviculture, Zhejiang A&F University, Lin'an, Zhejiang, China
Genet Mol Res. 2016 Aug 19;15(3):gmr8515. doi: 10.4238/gmr.15038515.
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.
Ty3-gypsy长末端重复逆转座子在许多植物基因组中普遍存在。本研究报道了四种代表性竹种中存在异质Ty3-gypsy逆转座子：毛竹（Phyllostachys heterocycla (Carr.) Mitford cv. pubescens）、龟甲竹（P. heterocycla (Carr.) Mitford cv. heterocycla）、绿竹（Dendrocalamopsis oldhami）和倭竹（Pleioblastus fortunei）。使用对应于Ty3-gypsy逆转座子逆转录酶（rt）基因保守结构域的简并寡核苷酸引物，从基因组DNA中扩增出165个不同的序列。核苷酸序列长度从366到438 bp不等。这些序列表现出高度的异质性，同源性范围为52.2%至99.8%。构建了一个系统发育树，包括拟南芥（Arabidopsis thaliana）和水稻（Oryza sativa）。竹子Ty3-gypsy序列形成了三个不同的逆转座子簇（gypsy I-III）。进一步分析表明，不仅在远缘物种中发现了几乎相同的Ty3-gypsy逆转座子，而且在近缘物种中也观察到了高度多样的Ty3-gypsy逆转座子。本研究结果提供了有关竹子基因组的遗传和进化信息，这可能有助于进一步研究竹子以及其他物种中的重复元件。
