Shen Xin, Ma Xiaoyin, Ren Jianfeng, Zhao Fangqing
Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, PR China.
BMC Genomics. 2009 Mar 28;10:136. doi: 10.1186/1471-2164-10-136.
There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum.
The mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups.
This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.
完整线粒体（mt）基因组在准确重建后生动物系统发育关系方面具有诸多优势。尽管已有超过一千个后生动物基因组被测序，但分类取样存在高度偏差，许多门类没有一个完整线粒体基因组的代表。星虫动物门（花生虫或星虫）是一类小型的蠕虫状海洋生物分类群，其系统发育位置尚不确定。在本报告中，我们展示了可口革囊星虫的线粒体基因组序列，这是该门的首个完整线粒体基因组。
可口革囊星虫的线粒体基因组长度为15,494 bp。编码链由32.1%的A、21.5%的C、13.0%的G和33.4%的T碱基组成（AT = 65.5%；AT偏斜 = -0.019；GC偏斜 = -0.248）。它包含13个蛋白质编码基因（PCGs），总共3709个密码子，22个转运RNA基因，2个核糖体RNA基因和一个富含AT的非编码区（AT = 74.2%）。所有37个已鉴定的基因都从同一条DNA链转录。与典型的后生动物线粒体基因组相比，星虫动物门缺少trnR但有一个额外的trnM。对蛋白质序列的最大似然法和贝叶斯分析表明，吸口虫纲、星虫动物门和环节动物门（包括螠虫动物门和须腕动物门）形成一个单系类群，这支持了星虫动物门与环节动物门之间的关系比与软体动物门、腕足动物门和其他一些触手冠动物类群更为密切。
这是星虫动物门内作为代表的完整线粒体基因组的首次报告。它与四个已知的环节动物和一个螠虫动物的线粒体DNA有更多相似特征。首先，星虫动物门和环节动物门在线粒体基因组中的基因排列非常相似，所有37个基因都位于同一条链上；其次，基于串联蛋白质序列的系统发育分析也有力地支持了星虫动物门 + 环节动物门分支（包括螠虫动物门和须腕动物门）。因此，包括分节在内的环节动物“关键特征”可能比以前认为的更不稳定。
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