Deng Hongyuan, Shu Dan, Luo Di, Gong Tao, Sun Fenghui, Tan Hong
Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, The Chinese Academy of Sciences, Chengdu, China; University of the Chinese Academy of Sciences, Beijing, China.
J Basic Microbiol. 2013 Oct;53(10):815-22. doi: 10.1002/jobm.201200238. Epub 2013 Jun 17.
Miniature inverted-repeat transposable elements (MITEs) are short non-autonomous DNA transposons that play an important role in genome structure and function. Here, we described a novel family of MITEs, named Scatter, identified from the genomes of three strains of the fungus Botrytis cinerea (T4, B05.10, and TBC-A). Intact Scatter elements are typically an average of 247 bp, and contain 41 bp terminal inverted repeats (TIRs) and 2-bp "TA" target site duplications (TSDs). Based a search against the transposable elements database and GenBank, Scatter is a novel and potentially species-specific family of MITEs. Moderate heterogeneity in sequence and size of individual Scatter copies suggests that Scatter elements were not recently proliferated. Most integrated sites were conserved across all three strains tested and elements inserted at equivalent sites shared high identity at the nucleotide level. This conservation, in combination with the presence of a similar copy number (22-24), in B. cinerea strains tested suggests that Scatter may be a relic of an ancient transposition developed prior to the strain divergence of B. cinerea. Two unique insertion instances were observed, indicating that some copies of Scatter may have remained active following strain divergence of B. cinerea. Because only a few subtle insertion differences among B. cinerea strains were observed, Scatter may play only a minor role in the genetic diversity in B. cinerea species. Most Scatter elements appear to be inserted in potential regulatory regions of adjacent coding regions, highlighting their role in transcriptional regulation. The origin of Scatter remains to be addressed. Scatter is the first well-characterized family of MITEs in B. cinerea.
微型反向重复转座元件（MITEs）是短的非自主DNA转座子，在基因组结构和功能中发挥重要作用。在此，我们描述了一个新的MITEs家族，命名为Scatter，它是从三种灰葡萄孢菌株（T4、B05.10和TBC - A）的基因组中鉴定出来的。完整的Scatter元件通常平均长度为247 bp，包含41 bp的末端反向重复序列（TIRs）和2 bp的“TA”靶位点重复序列（TSDs）。基于对转座元件数据库和GenBank的搜索，Scatter是一个新的且可能具有物种特异性的MITEs家族。单个Scatter拷贝在序列和大小上存在适度的异质性，这表明Scatter元件并非近期增殖而来。在所有测试的三种菌株中，大多数整合位点是保守的，并且插入到等效位点的元件在核苷酸水平上具有高度同一性。这种保守性，再加上在测试的灰葡萄孢菌株中存在相似的拷贝数（22 - 24个），表明Scatter可能是灰葡萄孢菌株分化之前古老转座事件的遗迹。观察到两个独特的插入实例，表明在灰葡萄孢菌株分化后，一些Scatter拷贝可能仍然具有活性。由于在灰葡萄孢菌株之间仅观察到一些细微的插入差异，Scatter可能在灰葡萄孢物种的遗传多样性中仅起次要作用。大多数Scatter元件似乎插入到相邻编码区的潜在调控区域，突出了它们在转录调控中的作用。Scatter的起源仍有待研究。Scatter是灰葡萄孢中第一个得到充分表征的MITEs家族。
