Ahmed Salim, Shafiuddin Md, Azam Muhammad Shafiul, Islam Md Shahidul, Ghosh Ajit, Khan Haseena
Department of Genetic Engineering and Biotechnology; University of Dhaka; Dhaka, Bangladesh.
Mob Genet Elements. 2011 May;1(1):18-28. doi: 10.4161/mge.1.1.16433.
Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1,250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.
长末端重复序列（LTR）逆转座子是真核生物基因组的重要组成部分，在基因组进化中发挥着重要作用，尤其是在植物中。黄麻是一种重要的纤维作物，其基因组庞大，达1250兆碱基对。该基因组大部分仍未被探索。在本研究中，我们旨在鉴定和表征黄麻的LTR逆转座子，以便更好地了解黄麻基因组。在本研究中，通过简并引物扩增了黄麻Ty1-copia和Ty3-gypsy LTR逆转座子的逆转录酶结构域，并通过逆转录PCR检测了它们的表达。通过斑点杂交分析确定了Ty1-copia和Ty3-gypsy元件逆转录酶（RT）基因的拷贝数。序列分析显示，Ty1-copia逆转座子之间的异质性高于Ty3-gypsy，并将它们各自聚类为三组。从斑点杂交中发现，Ty1-copia中RT基因的拷贝数高于Ty(^3)-gypsy元件。累积起来，Ty1-copia和Ty3-gypsy可能占黄麻基因组的19%左右，其中两组Ty1-copia被发现具有转录活性。由于LTR逆转座子构成了黄麻基因组的很大一部分，这些发现暗示了这些元件在黄麻基因组进化中的重要性。
