The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features.
The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features.
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DOI：
10.1186/1471-2164-7-241
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发表时间：
2006-09-20
期刊：
影响因子：
4.4
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中科院分区：
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线粒体基因组的序列数据和其他特征（基因易位，RNA分子的二级结构）在从种群到门水平的后生动物系统发育研究中是有用的。此外，完整线粒体序列的比较为小基因组的进化提供了有价值的信息，例如基因易位、基因复制和基因丢失的不同机制，或核苷酸频率偏差。甲壳纲（类、等足类等）包括约21,000种甲壳类动物，生活在从深海到干旱陆地栖息地的许多环境中。大洋狮是一种陆生等足类动物，生活在欧洲北海和大西洋海岸线的岩石海岸。这项研究揭示了首个来自过硬壳类动物的完整线粒体DNA序列。海洋Ligia oceanica线粒体基因组是一个环状双链DNA分子，大小为15,289 bp。与其他甲壳类动物相比，它显示了线粒体基因顺序的一些变化。本文还对所有甲壳类动物的线粒体基因序列进行了综述。出乎意料的是，与基因组的其余部分相比，大洋Ligia线粒体基因组中最大的非编码部分（假定的线粒体控制区）并不富含at。它具有两个重复区（4× 10 bp和3× 64 bp），具有富含gc的发夹状二级结构。一些转移rna显示二级结构，源自通常的三叶草模式。虽然一些tRNA基因被认为是RNA编辑的靶标，但trnR根本无法定位。基因顺序在甲壳目动物中不保守，甚至在等足类动物中也不保守。与节肢动物的陆地模式和片足动物的夏威夷Parhyale相比，两个等足动物物种Ligia oceanica和Idotea baltica显示出相似的衍生基因顺序，这表明大多数易位事件已经出现在这些等足动物的最后共同祖先中。除此之外，三个tRNA基因的位置在两个等足类物种中也有所不同。与其他马甲类动物相比，这两种等足类动物的核苷酸频率的链偏倚是相反的。这可能是由于复制起源的逆转，与其他甲壳类动物相比，在控制区域发现的典型发夹结构在等足类动物中显示出相反的方向，这一事实进一步支持了这一点。
Sequence data and other characters from mitochondrial genomes (gene translocations, secondary structure of RNA molecules) are useful in phylogenetic studies among metazoan animals from population to phylum level. Moreover, the comparison of complete mitochondrial sequences gives valuable information about the evolution of small genomes, e.g. about different mechanisms of gene translocation, gene duplication and gene loss, or concerning nucleotide frequency biases. The Peracarida (gammarids, isopods, etc.) comprise about 21,000 species of crustaceans, living in many environments from deep sea floor to arid terrestrial habitats. Ligia oceanica is a terrestrial isopod living at rocky seashores of the european North Sea and Atlantic coastlines. The study reveals the first complete mitochondrial DNA sequence from a peracarid crustacean. The mitochondrial genome of Ligia oceanica is a circular double-stranded DNA molecule, with a size of 15,289 bp. It shows several changes in mitochondrial gene order compared to other crustacean species. An overview about mitochondrial gene order of all crustacean taxa yet sequenced is also presented. The largest non-coding part (the putative mitochondrial control region) of the mitochondrial genome of Ligia oceanica is unexpectedly not AT-rich compared to the remainder of the genome. It bears two repeat regions (4× 10 bp and 3× 64 bp), and a GC-rich hairpin-like secondary structure. Some of the transfer RNAs show secondary structures which derive from the usual cloverleaf pattern. While some tRNA genes are putative targets for RNA editing, trnR could not be localized at all. Gene order is not conserved among Peracarida, not even among isopods. The two isopod species Ligia oceanica and Idotea baltica show a similarly derived gene order, compared to the arthropod ground pattern and to the amphipod Parhyale hawaiiensis, suggesting that most of the translocation events were already present the last common ancestor of these isopods. Beyond that, the positions of three tRNA genes differ in the two isopod species. Strand bias in nucleotide frequency is reversed in both isopod species compared to other Malacostraca. This is probably due to a reversal of the replication origin, which is further supported by the fact that the hairpin structure typically found in the control region shows a reversed orientation in the isopod species, compared to other crustaceans.