Xu Yingxiu, Du Jianchang
Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China.
Plant J. 2014 Nov;80(4):582-91. doi: 10.1111/tpj.12656. Epub 2014 Sep 24.
Long terminal repeat (LTR) retrotransposons are the major DNA components of flowering plants. They are generally enriched in pericentromeric heterochromatin regions of their host genomes, which could result from the preferential insertion of LTR retrotransposons and the low effectiveness of purifying selection in these regions. To estimate the relative importance of the actions of these two factors on their distribution pattern, the LTR retrotransposons in Solanum lycopersicum (tomato) plants were characterized at the genome level, and then the distribution of young elements was compared with that of relatively old elements. The current data show that old elements are mainly located in recombination-suppressed heterochromatin regions, and that young elements are preferentially located in the gene-rich euchromatic regions. Further analysis showed a negative correlation between the insertion time of LTR retrotransposons and the recombination rate. The data also showed there to be more solo LTRs in genic regions than in intergenic regions or in regions close to genes. These observations indicate that, unlike in many other plant genomes, the current LTR retrotransposons in tomatoes have a tendency to be preferentially located into euchromatic regions, probably caused by their severe suppression of activities in heterochromatic regions. These elements are apt to be maintained in heterochromatin regions, probably as a consequence of the pericentromeric effect in tomatoes. These results also indicate that local recombination rates and intensities of purifying selection in different genomic regions are largely responsible for structural variation and non-random distribution of LTR retrotransposons in tomato plants.
长末端重复序列（LTR）反转录转座子是开花植物的主要DNA成分。它们通常富集于其宿主基因组的着丝粒周围异染色质区域，这可能是由于LTR反转录转座子的优先插入以及这些区域中纯化选择的低效性所致。为了评估这两个因素的作用对其分布模式的相对重要性，在基因组水平上对番茄植株中的LTR反转录转座子进行了表征，然后将年轻元件的分布与相对古老元件的分布进行了比较。目前的数据表明，古老元件主要位于重组抑制的异染色质区域，而年轻元件则优先位于富含基因的常染色质区域。进一步分析表明，LTR反转录转座子的插入时间与重组率之间呈负相关。数据还表明，基因区域中的单独LTR比基因间区域或靠近基因的区域更多。这些观察结果表明，与许多其他植物基因组不同，番茄中当前的LTR反转录转座子倾向于优先定位到常染色质区域，这可能是由于它们在异染色质区域的活性受到严重抑制所致。这些元件易于在异染色质区域中维持，这可能是番茄着丝粒效应的结果。这些结果还表明，不同基因组区域的局部重组率和纯化选择强度在很大程度上决定了番茄植株中LTR反转录转座子的结构变异和非随机分布。
