Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes
Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes
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DOI：
10.1016/j.fgb.2010.09.002
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发表时间：
2011-03-01
影响因子：
3
通讯作者：
Clutterbuck, A. John
中科院分区：
文献类型：
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作者：
Clutterbuck, A. John
通过两种独立的方法检查了 49 种丝状子囊菌（Pezizomycotina 亚门）的基因组，以寻找 RIP 典型的多个 C -> T 转变的证据。每个基因组中至少鉴定出一个转座元件或其他重复家族，并评估成员相对于其完整祖细胞模型的转变和颠换突变。当家庭成员因方向转变超过颠换而存在差异时，表明 RIP 的发生。通过考虑 CpG 和 CpC 二核苷酸双突变的算法对过渡突变进行量化。第二种方法评估整个基因组中的二核苷酸频率分布异常，该程序允许对遭受广泛定向突变的非编码基因组部分进行量化。两种方法的结果表明，RIP 样活性在突变程度和 C -> T 转换的二核苷酸背景上差异很大。在最极端的情况下，皮炎芽生菌基因组的 75% 出现了明显的 GC 缺失，且全部位于非编码部分。许多基因组既携带完整的重复序列，也携带其他因转变而遭受严重影响的重复序列。只有一种物种——球毛壳菌（Chaetomium globosum）没有表现出定向突变的证据。 (C) 2010 Elsevier Inc. 保留所有权利。
The genomes of 49 filamentous ascomycetes (subphylum Pezizomycotina) were examined by two independent methods for evidence of multiple C -> T transitions typical of RIP. At least one transposable element or other repeat family was identified in each genome, and members were assessed for transition and transversion mutations relative to a model of their intact progenitor. Occurrence of RIP was indicated where family members differed by excess of directional transitions over transversions. Transition mutations were quantified by an algorithm taking double mutations in CpG and CpC dinucleotides into account. A second method assessed dinucleotide frequency distribution anomalies in whole genomes, a procedure that allowed quantification of fractions of the non-coding genome that had been subject to extensive directional mutation. The results of both methods revealed that RIP-like activity varied greatly, both in extent of mutation and in dinucleotide context for C -> T transitions. In the most extreme case, 75% of a Blastomyces dermatitidis genome had suffered conspicuous GC-depletion, all of it in the non-coding fraction. Many genomes carried both intact repeats as well as others that had suffered heavily from transitions. Only one species, Chaetomium globosum, showed no evidence of directional mutation. (C) 2010 Elsevier Inc. All rights reserved.