Key Laboratory of Marine Bio-resource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
Gene. 2012 Oct 10;507(2):112-8. doi: 10.1016/j.gene.2012.07.032. Epub 2012 Jul 27.
A feasible way to perform evolutionary analyses is to compare characters divergent enough to observe significant differences, but sufficiently similar to exclude saturation of the differences that occurred. Thus, comparisons of invertebrate mitochondrial (mt) genomes at low taxonomic levels can be extremely helpful in investigating patterns of variation and evolutionary dynamics of genomes, as intermediate stages of the process may be identified. Fortunately, in this study, we newly sequenced the mt genome of the eighth member of Asian Crassostrea oysters which can provide necessary intermediate characters for us to believe that the variation of Crassostrea mt genomes is considerably greater than previously acknowledged. Several new features of Asian Crassostrea oyster mitochondrial genomes were revealed, and our results are particularly significant as they 1) suggest a novel model of alloacceptor tRNA gene recruitment, namely "vertical" tRNA gene recruitment, which can be successfully used to explain the origination of the unusually additional trnK and trnQ genes (annotated as trnK(2) and trnQ(2) respectively) in the mt genomes of the five Asian oysters, and we speculate that this recruitment progress may be a common phenomenon in the evolution of the tRNA multigene family; 2) reveal the existence of two additional, lineage-specific, mtDNA-encoded genes that may originate from duplication of nad2 followed by rapid evolutionary change. Each of these two genes encodes a unique amino terminal signal peptide, thus each might possess an unknown function; and 3) identify for the first time the atp8 gene in oysters. The present study thus gives further credence to the comparison of congeneric bivalves as a meaningful strategy to investigate mt genomic evolutionary trends in genome organization, tRNA multigene family, and gene loss and/or duplication that are difficult to undertake at higher taxonomic levels. In particular, our study provides new evidence for the identification and characterization of ORFs in the "non-coding region" of animal mt genomes.
进行进化分析的一种可行方法是比较足够发散以观察到显著差异的特征，但又要足够相似以排除已发生差异的饱和。因此，在低分类学水平上比较无脊椎动物线粒体 (mt) 基因组对于研究基因组的变异和进化动态非常有帮助，因为可以确定中间阶段。幸运的是，在本研究中，我们新测序了亚洲牡蛎第八个成员的 mt 基因组，这为我们提供了必要的中间特征，使我们相信牡蛎 mt 基因组的变异比以前认为的要大得多。亚洲牡蛎线粒体基因组的几个新特征被揭示出来，我们的结果尤其重要，因为它们 1）提出了一种新的 alloacceptor tRNA 基因募集模型，即“垂直”tRNA 基因募集，它可以成功地用于解释五个亚洲牡蛎 mt 基因组中异常额外的 trnK 和 trnQ 基因（分别注释为 trnK(2) 和 trnQ(2)）的起源，我们推测这种募集过程可能是 tRNA 多基因家族进化中的一个常见现象；2）揭示了两个额外的、谱系特异性的 mtDNA 编码基因的存在，这些基因可能起源于 nad2 的复制，随后发生快速进化变化。这两个基因中的每一个都编码一个独特的氨基末端信号肽，因此每个基因可能具有未知的功能；3）在牡蛎中首次鉴定出 atp8 基因。本研究进一步证明了同种双壳类动物的比较是一种有意义的策略，可以研究基因组组织、tRNA 多基因家族以及在更高分类学水平上难以进行的基因丢失和/或复制的 mt 基因组进化趋势。特别是，我们的研究为鉴定和表征动物 mt 基因组“非编码区”中的 ORFs 提供了新的证据。
