The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships.
The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships.
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DOI：
10.1186/1471-2164-12-572
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发表时间：
2011-11-23
期刊：
影响因子：
4.4
通讯作者：
Hausdorf B
中科院分区：
文献类型：
--
作者：
Nesnidal MP;Helmkampf M;Bruchhaus I;Hausdorf B
直肠类、腕足类和裸足类在纤毛虫中的系统发育关系仍存在争议。我们对物种最丰富的脊椎动物--外肠动物--的额外线粒体基因组进行了测序。虽然已知不同谱系的线粒体序列的核苷酸组成以及编码蛋白的氨基酸组成存在很大差异，但在系统发育分析中往往不考虑这种偏见。我们在线粒体序列的系统发育分析中应用了几种减少组成偏差和饱和度的方法。测定了水蚤的线粒体全基因组序列(16,089bp)。所有编码蛋白质、rRNA和tRNA的基因都是从同一条链转录而来的。Flustra与唇口类外直肠Bugula有很长的基因间序列，这可能是这些分类群的同形同构体。进一步的突触构型可能是tRNA L(UUR)的Dhu臂的丢失，tRNA S(Ucn)的Dhu臂的丢失(Ucn)和tRNA L(Cun)的独特的反密码子序列Gag的丢失。线虫线粒体基因组的基因序列与其他已知的外直肠动物有很大的不同。线粒体核苷酸和氨基酸数据集的系统发育分析表明，轮虫血统与轮虫门的亲缘关系比与后口或蜕皮虫的亲缘关系更近，证实了轮虫的假说。此外，它们还支持单口门和外直肠门。然而，根据数据集和使用的方法，Lophotrochozoa内的轮虫谱系之间的关系有很大的不同。减少核苷酸和氨基酸数据集的异质性和饱和度的不同方法并不会导致更稳健地解决Lophotrochozoan关系。基于线粒体序列对钩虫门之间相互矛盾且通常缺乏支持的系统发育重建表明，这些单独包含的信息不足以有力地解决钩虫门之间的关系。线粒体基因序列也不能用来推断它们的系统发育关系，因为它在外直肠动物、腕足类和其他一些轮虫纲中是高度不同的。然而，我们的研究发现了一些罕见的基因组变化，如长基因间序列的进化和tRNAs结构的变化，这可能有助于重建外直肠动物的系统发育。
The phylogenetic relationships of the lophophorate lineages, ectoprocts, brachiopods and phoronids, within Lophotrochozoa are still controversial. We sequenced an additional mitochondrial genome of the most species-rich lophophorate lineage, the ectoprocts. Although it is known that there are large differences in the nucleotide composition of mitochondrial sequences of different lineages as well as in the amino acid composition of the encoded proteins, this bias is often not considered in phylogenetic analyses. We applied several approaches for reducing compositional bias and saturation in the phylogenetic analyses of the mitochondrial sequences. The complete mitochondrial genome (16,089 bp) of Flustra foliacea (Ectoprocta, Gymnolaemata, Cheilostomata) was sequenced. All protein-encoding, rRNA and tRNA genes are transcribed from the same strand. Flustra shares long intergenic sequences with the cheilostomate ectoproct Bugula, which might be a synapomorphy of these taxa. Further synapomorphies might be the loss of the DHU arm of the tRNA L(UUR), the loss of the DHU arm of the tRNA S(UCN) and the unique anticodon sequence GAG of the tRNA L(CUN). The gene order of the mitochondrial genome of Flustra differs strongly from that of the other known ectoprocts. Phylogenetic analyses of mitochondrial nucleotide and amino acid data sets show that the lophophorate lineages are more closely related to trochozoan phyla than to deuterostomes or ecdysozoans confirming the Lophotrochozoa hypothesis. Furthermore, they support the monophyly of Cheilostomata and Ectoprocta. However, the relationships of the lophophorate lineages within Lophotrochozoa differ strongly depending on the data set and the used method. Different approaches for reducing heterogeneity in nucleotide and amino acid data sets and saturation did not result in a more robust resolution of lophotrochozoan relationships. The contradictory and usually weakly supported phylogenetic reconstructions of the relationships among lophotrochozoan phyla based on mitochondrial sequences indicate that these alone do not contain enough information for a robust resolution of the relations of the lophotrochozoan phyla. The mitochondrial gene order is also not useful for inferring their phylogenetic relationships, because it is highly variable in ectoprocts, brachiopods and some other lophotrochozoan phyla. However, our study revealed several rare genomic changes like the evolution of long intergenic sequences and changes in the structure of tRNAs, which may be helpful for reconstructing ectoproct phylogeny.
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