The mitochondrial genome of a deep-sea bamboo coral (Cnidaria, Anthozoa, Octocorallia, Isididae): Genome structure and putative origins of replication are not conserved among octocorals
The mitochondrial genome of a deep-sea bamboo coral (Cnidaria, Anthozoa, Octocorallia, Isididae): Genome structure and putative origins of replication are not conserved among octocorals
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DOI：
10.1007/s00239-008-9116-2
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发表时间：
2008-08-01
影响因子：
3.9
通讯作者：
France, Scott C.
中科院分区：
文献类型：
--
作者：
Brugler, Mercer R.;France, Scott C.
珊瑚线粒体（mt）DNA的替换率非常低，有人认为mt基因组的内容和结构在整个亚类中是保守的，这一观察结果得到了大多数珊瑚科的支持，通过使用跨越基因边界的PCR产物进行系统发育分析。然而，未能恢复跨越的nad 4L-msh 1基因连接的物种从家庭Isididae（竹珊瑚）的扩增产物，促使我们测序完整的MT基因组的深海竹珊瑚（未描述的物种）。与“典型的”竹珊瑚mt基因组相比，它有12个基因转录在一条链上，5个基因转录在相反的链上（cox 2，atp 8，atp 6，cox 3，trnM），在竹珊瑚基因组中，一个连续的5个基因（msh 1，rnl，nad 2，nad 5，nad 4）串经历了反转，可能在一个单一的事件。链特异性组成不对称性的分析表明，（i）轻链复制起点也被反转，并与nad 4相邻，（ii）重链复制起点（OriH）的方向相对于先前已知的珊瑚mt基因组反转。比较分析表明，线粒体内的重组和错误的复制OriH可能是负责的基因顺序的变化，在珊瑚和hexacorals，分别。使用引物侧翼的区域在任何一端的倒五个基因集，我们研究了密切相关的类群，并确定新的基因顺序仅限于深海亚科Keratoisidinae;然而，我们没有发现任何证据链特异性突变的偏见，可能会影响系统发育分析，包括这个亚科的竹珊瑚。
Octocoral mitochondrial (mt) DNA is subject to an exceptionally low rate of substitution, and it has been suggested that mt genome content and structure are conserved across the subclass, an observation that has been supported for most octocorallian families by phylogenetic analyses using PCR products spanning gene boundaries. However, failure to recover amplification products spanning the nad4L-msh1 gene junction in species from the family Isididae (bamboo corals) prompted us to sequence the complete mt genome of a deep-sea bamboo coral (undescribed species). Compared to the "typical" octocoral mt genome, which has 12 genes transcribed on one strand and 5 genes on the opposite (cox2, atp8, atp6, cox3, trnM), in the bamboo coral genome a contiguous string of 5 genes (msh1, rnl, nad2, nad5, nad4) has undergone an inversion, likely in a single event. Analyses of strand-specific compositional asymmetry suggest that (i) the light-strand origin of replication was also inverted and is adjacent to nad4, and (ii) the orientation of the heavy-strand origin of replication (OriH) has reversed relative to that of previously known octocoral mt genomes. Comparative analyses suggest that intramitochondrial recombination and errors in replication at OriH may be responsible for changes in gene order in octocorals and hexacorals, respectively. Using primers flanking the regions at either end of the inverted set of five genes, we examined closely related taxa and determined that the novel gene order is restricted to the deep-sea subfamily Keratoisidinae; however, we found no evidence for strand-specific mutational biases that may influence phylogenetic analyses that include this subfamily of bamboo corals.