Xu Jinshan, Pan Guoqing, Fang Lin, Li Jun, Tian Xiangjun, Li Tian, Zhou Zeyang, Xiang Zhonghuai
The Key Sericultural Laboratory of Agricultural Ministry of China, Southwest University, Beibei, Chongqing 400716, China.
Int J Parasitol. 2006 Aug;36(9):1049-56. doi: 10.1016/j.ijpara.2006.04.010. Epub 2006 May 30.
Microsporidia are a group of intracellular parasites with an extremely compact genome and there is no confirmed evidence that retroelements are parasitised in these organisms. Using the dataset of 200,000 genomic shotgun reads of the silkworm pebrine Nosema bombycis, we have identified the eight complete N. bombycis long-terminal repeat retrotransposon (Nbr) elements. All of the Nbr elements are Ty3/gypsy members and have close relationships to Saccharomycetes long-terminal repeat retrotransposons identified previously, providing further evidence of their relationship to fungi. To explore the effect of retrotransposons in microsporidian genome evolution, their distribution was characterised by comparisons between two N. bombycis contigs containing the Nbr elements with the completed genome of the human parasite Encephalitozoon cuniculi, which is closely related to N. bombycis. The Nbr elements locate between or beside syntenic blocks, which are often clustered with other transposable-like sequences, indicating that they are associated with genome size variation and syntenic discontinuities. The ratios of the number of non-synonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site of the open reading frames among members of each of the eight Nbr families were estimated, which reveal the purifying selection acted on the N. bombycis long-terminal repeat retrotransposons. These results strongly suggest that retrotransposons play a major role in reorganization of the microsporidian genome and they might be active. The present study presents an initial characterization of some transposable elements in the N. bombycis genome and provides some insight into the evolutionary mechanism of microsporidian genomes.
微孢子虫是一类细胞内寄生虫，其基因组极其紧凑，目前尚无确凿证据表明反转录元件寄生在这些生物体内。利用家蚕微粒子病病原体家蚕微孢子虫（Nosema bombycis）200,000条基因组鸟枪法测序读段的数据集，我们鉴定出了8个完整的家蚕微孢子虫长末端重复反转录转座子（Nbr）元件。所有Nbr元件均为Ty3/gypsy家族成员，且与先前鉴定出的酵母菌长末端重复反转录转座子关系密切，进一步证明了它们与真菌的关系。为了探究反转录转座子在微孢子虫基因组进化中的作用，通过比较两个含有Nbr元件的家蚕微孢子虫重叠群与人类寄生虫兔脑炎微孢子虫（Encephalitozoon cuniculi）的完整基因组（兔脑炎微孢子虫与家蚕微孢子虫关系密切），对其分布特征进行了研究。Nbr元件位于同线基因块之间或旁边，它们常与其他类似转座的序列聚集在一起，这表明它们与基因组大小变异和同线基因不连续性有关。估计了8个Nbr家族各成员开放阅读框中每非同义位点非同义替换数与每同义位点同义替换数的比率，结果显示纯化选择作用于家蚕微孢子虫长末端重复反转录转座子。这些结果有力地表明，反转录转座子在微孢子虫基因组重组中起主要作用，且它们可能具有活性。本研究对家蚕微孢子虫基因组中的一些转座元件进行了初步表征，并为微孢子虫基因组的进化机制提供了一些见解。
