Department of Biological and Environmental Sciences, University ofGothenburg, PO Box 463, SE-405 30 Gothenburg, Sweden.
BMC Genomics. 2012 Apr 17;13:139. doi: 10.1186/1471-2164-13-139.
The mitochondrial genome is important for studying genome evolution as well as reconstructing the phylogeny of organisms. Complete mitochondrial genome sequences have been reported for more than 2200 metazoans, mainly vertebrates and arthropods. To date, from a total of about 1275 described nemertean species, only three complete and two partial mitochondrial DNA sequences from nemerteans have been published. Here, we report the entire mitochondrial genomes for two more nemertean species: Nectonemertes cf. mirabilis and Zygeupolia rubens.
The sizes of the entire mitochondrial genomes are 15365 bp for N. cf. mirabilis and 15513 bp for Z. rubens. Each circular genome contains 37 genes and an AT-rich non-coding region, and overall nucleotide composition is AT-rich. In both species, there is significant strand asymmetry in the distribution of nucleotides, with the coding strand being richer in T than A and in G than C. The AT-rich non-coding regions of the two genomes have some repeat sequences and stem-loop structures, both of which may be associated with the initiation of replication or transcription. The 22 tRNAs show variable substitution patterns in nemerteans, with higher sequence conservation in genes located on the H strand. Gene arrangement of N. cf. mirabilis is identical to that of Paranemertes cf. peregrina, both of which are Hoplonemertea, while that of Z. rubens is the same as in Lineus viridis, both of which are Heteronemertea. Comparison of the gene arrangements and phylogenomic analysis based on concatenated nucleotide sequences of the 12 mitochondrial protein-coding genes revealed that species with closer relationships share more identical gene blocks.
The two new mitochondrial genomes share many features, including gene contents, with other known nemertean mitochondrial genomes. The tRNA families display a composite substitution pathway. Gene order comparison to the proposed ground pattern of Bilateria and some lophotrochozoans suggests that the nemertean ancestral mitochondrial gene order most closely resembles the heteronemertean type. Phylogenetic analysis proposes a sister-group relationship between Hetero- and Hoplonemertea, which supports one of two recent alternative hypotheses of nemertean phylogeny.
线粒体基因组对于研究基因组进化以及重建生物的系统发育非常重要。目前已经报道了超过 2200 种后生动物的完整线粒体基因组，主要是脊椎动物和节肢动物。迄今为止，在总共约 1275 种描述的纽形动物物种中，仅有三种纽形动物的完整和两种部分线粒体 DNA 序列已发表。在这里，我们报告了另外两种纽形动物的完整线粒体基因组：拟奇异美纽虫（Nectonemertes cf. mirabilis）和红纹纽虫（Zygeupolia rubens）。
完整的线粒体基因组大小分别为拟奇异美纽虫的 15365bp 和红纹纽虫的 15513bp。每个圆形基因组包含 37 个基因和一个富含 AT 的非编码区，整体核苷酸组成富含 AT。在这两个物种中，核苷酸的分布存在明显的链不对称性，编码链中 T 比 A 多，G 比 C 多。两个基因组的富含 AT 的非编码区都有一些重复序列和茎环结构，这两者都可能与复制或转录的起始有关。这两种纽形动物的 22 个 tRNA 显示出可变的替代模式，位于 H 链上的基因具有更高的序列保守性。拟奇异美纽虫的基因排列与扁形纽虫（Paranemertes cf. peregrina）相同，它们都属于游吻纽形动物门（Hoplonemertea），而红纹纽虫的基因排列与绿纽虫（Lineus viridis）相同，它们都属于真纽形动物门（Heteronemertea）。基于 12 个线粒体蛋白编码基因的核苷酸序列串联构建的基因排列比较和系统发育分析表明，亲缘关系较近的物种具有更多相同的基因块。
这两个新的线粒体基因组与其他已知的纽形动物线粒体基因组具有许多共同特征，包括基因组成。tRNA 家族显示出复合替代途径。与双胚层动物和一些担轮动物的假定原始模式进行基因排序比较表明，纽形动物的祖先线粒体基因排序最接近真纽形动物的类型。系统发育分析提出了真纽形动物门和游吻纽形动物门之间的姐妹群关系，这支持了纽形动物系统发育的两种最新替代假说之一。
