Kilpert Fabian, Podsiadlowski Lars
Department of Animal Systematics and Evolution, Institute of Biology, Freie Universität Berlin, Konigin-Luise-Str, 1-3, D-14195 Berlin, Germany.
BMC Genomics. 2006 Sep 20;7:241. doi: 10.1186/1471-2164-7-241.
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 (4x 10 bp and 3x 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.
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很有用。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，例如关于基因易位、基因重复和基因丢失的不同机制，或关于核苷酸频率偏差。囊虾总目（钩虾、等足类动物等）包括约21000种甲壳类动物，生活在从深海海底到干旱陆地栖息地的多种环境中。海滨漂水虱是一种生活在欧洲北海和大西洋海岸线岩石海岸的陆生等足类动物。
该研究揭示了首个来自囊虾总目甲壳类动物的完整线粒体DNA序列。海滨漂水虱的线粒体基因组是一个环状双链DNA分子，大小为15289 bp。与其他甲壳类物种相比，它的线粒体基因顺序有一些变化。还给出了所有已测序甲壳类分类群线粒体基因顺序的概述。海滨漂水虱线粒体基因组中最大的非编码部分（假定的线粒体控制区）与基因组的其余部分相比，出乎意料地并非富含AT。它有两个重复区域（4×10 bp和3×64 bp），以及一个富含GC的发夹样二级结构。一些转运RNA呈现出不同于常见三叶草结构的二级结构。虽然一些tRNA基因是RNA编辑的假定靶点，但trnR根本无法定位。
基因顺序在囊虾总目动物中并不保守，甚至在等足类动物中也不保守。与节肢动物基本模式和夏威夷半臂虾相比，海滨漂水虱和波罗的海麦秆虫这两种等足类动物显示出相似的衍生基因顺序，这表明大多数易位事件在这些等足类动物的最后一个共同祖先中就已经存在。除此之外，两种等足类动物中三个tRNA基因的位置不同。与其他软甲纲动物相比，两种等足类动物的核苷酸频率链偏向发生了反转。这可能是由于复制起点的反转，这一事实进一步支持了这一点，即与其他甲壳类动物相比，等足类动物中通常在控制区发现的发夹结构呈现出相反的方向。
