Sequence variation within the rRNA gene loci of 12 Drosophila species
Sequence variation within the rRNA gene loci of 12 Drosophila species
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DOI：
10.1101/gr.6376807
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发表时间：
2007-12-01
期刊：
影响因子：
7
通讯作者：
Eickbush, Thomas H.
中科院分区：
文献类型：
--
作者：
Stage, Deborah E.;Eickbush, Thomas H.
协同进化使任何真核生物中存在的数百个串联排列的核糖体 RNA (rRNA) 基因及其间隔区保持接近同一性。很少有全面的尝试来直接测量 rDNA 单位之间的同一性。我们使用通过 12 个果蝇物种的全基因组鸟枪测序项目获得的原始测序读数（跟踪档案）来定位 rDNA 单元 7.8-8.2 kb 转录部分内的序列变异。在 11 个物种的总 rDNA 单位的 3% 以上中发现了 3 到 18 个变异。 rDNA 单位存在于多个染色体上的物种仅表现出序列变异的微小增加。与 rDNA 单位的编码区相比，非编码区的变体丰富度高出 10-20 倍。在编码区内，与保守的核心区相比，扩展中的变体丰富度是三到八倍。变体的分布在很大程度上与协同进化模型一致，在协同进化模型中，单位的转录部分存在均匀的重组，且固定变体的频率取决于保留该序列的选择压力。然而，尽管 28S 基因的进化速度比 18S 基因快 2.5 倍，但其变异数却比 18S 基因少。我们假设 28S 基因中变异较少是由于专门用于插入这些物种的 28S 基因中的逆转录转座元件的活性触发的局部基因转换或 DNA 修复。
Concerted evolution maintains at near identity the hundreds of tandemly arrayed ribosomal RNA ( rRNA) genes and their spacers present in any eukaryote. Few comprehensive attempts have been made to directly measure the identity between the rDNA units. We used the original sequencing reads ( trace archives) available through the whole-genome shotgun sequencing projects of 12 Drosophila species to locate the sequence variants within the 7.8-8.2 kb transcribed portions of the rDNA units. Three to 18 variants were identified in >3% of the total rDNA units from 11 species. Species where the rDNA units are present on multiple chromosomes exhibited only minor increases in sequence variation. Variants were 10-20 times more abundant in the noncoding compared with the coding regions of the rDNA unit. Within the coding regions, variants were three to eight times more abundant in the expansion compared with the conserved core regions. The distribution of variants was largely consistent with models of concerted evolution in which there is uniform recombination across the transcribed portion of the unit with the frequency of standing variants dependent upon the selection pressure to preserve that sequence. However, the 28S gene was found to contain fewer variants than the 18S gene despite evolving 2.5-fold faster. We postulate that the fewer variants in the 28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species.