Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida.
Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida.
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DOI：
10.1186/s12862-018-1186-1
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发表时间：
2018-04-27
影响因子：
3.4
通讯作者：
Huchon D
中科院分区：
文献类型：
--
作者：
Arafat H;Alamaru A;Gissi C;Huchon D
完整的线粒体（mt）基因组已对数千种动物进行了测序，并且代表了许多进化研究的选择分子。尽管如此，一些动物群体的样本仍然不足。栉水母（Ctenophora）（栉水母）就是一个这样的例子，迄今为止，该门仅确定了两个完整的 mt 序列，该门涵盖了大约 1 个门。描述了 150-200 个物种。数据的缺乏源于该谱系中极快的 mt 进化速度，使引物设计和 DNA 扩增变得复杂。事实上，在迄今为止测序的两个栉水母 mt 基因组中，即 Mnemiopsis leidyi（Lobata 目）和 Pleurobrachia bachei（Cydippida 目）的基因组中，rRNA 和蛋白质编码基因都表现出非凡的尺寸减小，并且具有高度衍生的序列。此外，所有 tRNA、atp6 和 atp8 基因均不存在。为了确定其他栉水母是否具有这些特征，我们获得了三种底栖栉水母的完整 mt 基因组，这三种栉水母属于迄今为止未采样的扁贝目：Coeloplana loyai、Coeloplana yulianicorum 和 Vallicula multiformis。底栖栉水母的 mt 基因组揭示了在 Mnemiopsis 和 Pleurobrachia 中发现的相同特性，表明快速的进化速度是栉水母 mt 基因组的一般特征。我们的结果还表明，这种高进化率不仅影响核苷酸取代，而且影响基因重排。事实上，基因顺序在不同分类目的代表之间高度重新排列，其中它接近随机，但在扁形纲内也相当可变，其中腔体属和壁形纲属仅共享四个保守的同线性块。然而，这两个同属腔皮动物物种显示出完全相同的基因顺序。由于极端的进化速度，我们的系统发育分析无法解决栉水母在后生动物中的系统发育位置或不同栉水母目之间的关系。比较序列分析使我们能够纠正 Pleurobrachia mt 基因组的注释，确认该物种不存在 tRNA，存在两个 rRNA 基因，以及存在密码子 TGA 从色氨酸重新分配到丝氨酸的情况。由于 Platyctenida 是栉水门中的一个早期分化谱系，我们的研究结果表明上述 mt 特征是该门的祖先特征。本文的在线版本 (10.1186/s12862-018-1186-1) 包含补充材料，可供授权用户使用。
Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. Ctenophora (comb jellies) is one such example, with only two complete mt sequences determined hitherto for this phylum, which encompasses ca. 150–200 described species. This lack of data derives from the extremely fast mt evolutionary rate in this lineage, complicating primer design and DNA amplification. Indeed, in the two ctenophore mt genomes sequenced to date, i.e. those of Mnemiopsis leidyi (order Lobata) and Pleurobrachia bachei (order Cydippida), both rRNA and protein coding genes exhibit an extraordinary size reduction and have highly derived sequences. Additionally, all tRNAs, and the atp6 and atp8 genes are absent. In order to determine whether these characteristics are shared by other ctenophores, we obtained the complete mt genomes of three benthic ctenophores belonging to the so far unsampled order of Platyctenida: Coeloplana loyai, Coeloplana yulianicorum and Vallicula multiformis. The mt genomes of benthic ctenophores reveal the same peculiarities found in Mnemiopsis and Pleurobrachia, demonstrating that the fast evolutionary rate is a general trait of the ctenophore mt genomes. Our results also indicate that this high evolutionary rate not only affects the nucleotide substitution but also gene rearrangements. Indeed, gene order was highly rearranged among representatives of the different taxonomic orders in which it was close to random, but also quite variable within Platyctenida, in which the genera Coeloplana and Vallicula share only four conserved synteny blocks. However, the two congeneric Coeloplana species display exactly the same gene order. Because of the extreme evolutionary rate, our phylogenetic analyses were unable to resolve the phylogenetic position of ctenophores within metazoans or the relationships among the different Ctenophora orders. Comparative sequence-analyses allowed us to correct the annotation of the Pleurobrachia mt genome, confirming the absence of tRNAs, the presence of both rRNA genes, and the existence of a reassignment of codon TGA from tryptophan to serine for this species. Since Platyctenida is an early diverging lineage among Ctenophora, our findings suggest that the mt traits described above are ancestral characteristics of this phylum. The online version of this article (10.1186/s12862-018-1186-1) contains supplementary material, which is available to authorized users.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
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DOI：
10.1093/bioinformatics/btt509
发表时间：
2013-11-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Nawrocki EP;Eddy SR
通讯作者：
Eddy SR
影响因子：
3.3
作者：
Rubinstein ND;Feldstein T;Shenkar N;Botero-Castro F;Griggio F;Mastrototaro F;Delsuc F;Douzery EJ;Gissi C;Huchon D
通讯作者：
Huchon D
影响因子：
4.1
作者：
Podar, M;Haddock, SHD;Harbison, GR
通讯作者：
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影响因子：
10.7
作者：
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通讯作者：
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