CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
Gene. 2014 Jan 1;533(1):439-46. doi: 10.1016/j.gene.2013.09.077. Epub 2013 Sep 29.
In contrast to the extreme conservation of nuclear-encoded tRNAs, organization of the mitochondrial (mt) tRNA gene family in invertebrates is highly dynamic and rapidly evolving. While gene duplication and loss, gene isomerism, recruitment, and rearrangements have occurred sporadically in several invertebrate lineages, little is known regarding the pattern of their evolution. Comparisons of invertebrate mt genomes at a generic level can be extremely helpful in investigating evolutionary patterns of variation, as intermediate stages of the process may be identified. Variation of mitochondrial tRNA organization among Meretrix clams provides good materials to investigate mt tRNA evolution. We characterized the complete mt genome of the lyrate Asiatic hard clam Meretrix lyrata, re-annotated tRNAs of four previously sequenced Meretrix clams, and undertook an intensive comparison of tRNA gene families in these clams. Our results 1) provide evidence that the commonly observed duplication of trnM may have occurred independently in different bivalve lineages and, based on the higher degree of trnM gene similarity, may have occurred more recently than expected; 2) suggest that "horizontal" evolution may have played an important role in tRNA gene family evolution based on frequent gene duplications and gene recruitment events; and 3) reveal the first case of isoacceptor "vertical" tRNA gene recruitment (VTGR) and present the first clear evidence that VTGR allows rapid evolution of tRNAs. We identify the trnS(-UCR) gene in Meretrix clams, previously considered missing in this lineage, and speculate that trnS(-UCR) lacking the D-arm in both M. lyrata and Meretrix lamarckii may represent the ancestral status. Phylogenetic analysis based on 13 concatenate protein-coding genes provided opportunities to detect rapidly evolved tRNA genes via VTGR and gene isomerism processes. This study suggests that evolution of the mt tRNA gene family in bivalves is more complex than previously thought and that comparison of several congeneric species is a useful strategy in investigating evolutionary patterns and dynamics of mt tRNA genes.
与核编码 tRNA 的极端保守性形成对比的是，无脊椎动物中线粒体 (mt) tRNA 基因家族的组织具有高度动态性和快速进化的特点。虽然基因复制和丢失、基因异构、招募和重排偶尔发生在几个无脊椎动物谱系中，但对于它们进化的模式知之甚少。在通用水平上比较无脊椎动物的 mt 基因组对于研究变异的进化模式非常有帮助，因为可能会识别出该过程的中间阶段。帘蛤科贻贝的线粒体 tRNA 组织的变化为研究 mt tRNA 进化提供了很好的材料。我们对褶纹冠蚌 Meretrix lyrata 的完整 mt 基因组进行了特征描述，重新注释了以前测序的四个帘蛤科贻贝的 tRNA，并对这些贻贝的 tRNA 基因家族进行了深入比较。我们的研究结果：1）提供了证据表明，trnM 常见的重复可能在不同的双壳类谱系中独立发生，并且基于更高程度的 trnM 基因相似性，可能比预期的更近；2）表明“水平”进化可能在 tRNA 基因家族进化中发挥了重要作用，这是基于频繁的基因复制和基因招募事件；3）揭示了第一个同工 tRNA 基因招募 (VTGR) 的案例，并首次提供了 VTGR 允许 tRNA 快速进化的明确证据。我们在帘蛤科贻贝中发现了以前被认为在该谱系中缺失的 trnS(-UCR)基因，并推测褶纹冠蚌和斑玉螺中缺乏 D 臂的 trnS(-UCR)可能代表祖先状态。基于 13 个串联蛋白编码基因的系统发育分析为通过 VTGR 和基因异构过程检测快速进化的 tRNA 基因提供了机会。本研究表明，双壳类动物 mt tRNA 基因家族的进化比以前想象的更为复杂，比较几个同种物种是研究 mt tRNA 基因进化模式和动态的有效策略。
