Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland,
Plant Cell Rep. 2013 Oct;32(10):1575-88. doi: 10.1007/s00299-013-1468-4. Epub 2013 Jun 11.
High heterogeneity was observed among conserved domains of reverse transcriptase ( rt ) isolated from quinoa. Only one Ty1- copia rt was highly amplified. Reverse transcriptase sequences were located predominantly in pericentromeric region of quinoa chromosomes. The heterogeneity, genomic abundance, and chromosomal distribution of reverse transcriptase (rt)-coding fragments of Ty1-copia and Ty3-gypsy long terminal repeat retrotransposons were analyzed in the Chenopodium quinoa genome. Conserved domains of the rt gene were amplified and characterized using degenerate oligonucleotide primer pairs. Sequence analyses indicated that half of Ty1-copia rt (51 %) and 39 % of Ty3-gypsy rt fragments contained intact reading frames. High heterogeneity among rt sequences was observed for both Ty1-copia and Ty3-gypsy rt amplicons, with Ty1-copia more heterogeneous than Ty3-gypsy. Most of the isolated rt fragments were present in quinoa genome in low copy numbers, with only one highly amplified Ty1-copia rt sequence family. The gypsy-like RNase H fragments co-amplified with Ty1-copia-degenerate primers were shown to be highly amplified in the quinoa genome indicating either higher abundance of some gypsy families of which rt domains could not be amplified, or independent evolution of this gypsy-region in quinoa. Both Ty1-copia and Ty3-gypsy retrotransposons were preferentially located in pericentromeric heterochromatin of quinoa chromosomes. Phylogenetic analyses of newly amplified rt fragments together with well-characterized retrotransposon families from other organisms allowed identification of major lineages of retroelements in the genome of quinoa and provided preliminary insight into their evolutionary dynamics.
在藜麦中分离的逆转录酶 ( rt ) 的保守结构域存在高度异质性。只有一个 Ty1- copia rt 被高度扩增。逆转录酶序列主要位于藜麦染色体的着丝粒周围区域。分析了 Ty1-copia 和 Ty3-gypsy 长末端重复逆转录转座子在藜麦基因组中的逆转录酶 (rt)-编码片段的异质性、基因组丰度和染色体分布。使用简并寡核苷酸引物对扩增和表征 rt 基因的保守结构域。序列分析表明，Ty1-copia rt 的一半 (51%) 和 Ty3-gypsy rt 片段的 39% 含有完整的阅读框。在 Ty1-copia 和 Ty3-gypsy rt 扩增子中都观察到 rt 序列的高度异质性，Ty1-copia 比 Ty3-gypsy 更具异质性。分离的 rt 片段大多数以低拷贝数存在于藜麦基因组中，只有一个高度扩增的 Ty1-copia rt 序列家族。与 Ty1-copia-简并引物共扩增的类 gypsy RNase H 片段在藜麦基因组中高度扩增，表明某些 gypsy 家族的丰度较高，其 rt 结构域无法扩增，或者该 gypsy 区域在藜麦中独立进化。Ty1-copia 和 Ty3-gypsy 逆转录转座子优先定位于藜麦染色体的着丝粒周围异染色质区。新扩增的 rt 片段与其他生物体中特征良好的逆转录转座子家族的系统发育分析允许鉴定藜麦基因组中逆转元件的主要谱系，并初步了解它们的进化动态。
