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Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements

机译：隐藻藻的线粒体基因组比较：基因改组和动态移动遗传元件

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Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax. The mitochondrial genomes were similar in terms of their general architecture, gene content and presence of a large repeat region. However, gene order was poorly conserved. Characteristic features of cryptophyte mtDNAs included large syntenic clusters resembling α-proteobacterial operons that encode bacteria-like rRNAs, tRNAs, and ribosomal protein genes. The cryptophyte mitochondrial genomes retain almost all genes found in many other eukaryotes including the nad, sdh, cox, cob, and atp genes, with the exception of sdh2 and atp3. In addition, gene cluster analysis showed that cryptophytes possess a gene order closely resembling the jakobid flagellates Jakoba and Reclinomonas. Interestingly, the cox1 gene of R. salina, T. amphioxeia, and Storeatula species was found to contain group II introns encoding a reverse transcriptase protein, as did the cob gene of Storeatula species CCMP1868. These newly sequenced genomes increase the breadth of data available from algae and will aid in the identification of general trends in mitochondrial genome evolution. While most of the genomes were highly conserved, extensive gene arrangements have shuffled gene order, perhaps due to genome rearrangements associated with hairpin-containing mobile genetic elements, tRNAs with palindromic sequences, and tandem repeat sequences. The cox1 and cob gene sequences suggest that introns have recently been acquired during cryptophyte evolution. Comparison of phylogenetic trees based on plastid and mitochondrial genome data sets underscore the different evolutionary histories of the host and endosymbiont components of present-day cryptophytes.
机译：隐藻是藻类的重要生态组成部分，由光养，异养和渗透性物种组成。该谱系对进化生物学家非常感兴趣，因为他们的质体是红色藻类次生共生共生体。隐植物对异养真核生物具有明显的系统发育亲和力，并具有四个基因组：宿主衍生的核和线粒体基因组，以及共生体的质体和核型基因组。为了深入了解隐藻线粒体的基因组进化，我们对五个物种的线粒体DNA进行了测序，并对以下隐藻属的七个基因组进行了比较分析：Chroomonas，Cryptomonas，Hemiselmis，Proteomonas，Rhodomonas，Storeatula和Teleaulax。线粒体基因组在总体结构，基因含量和大重复区域的存在方面相似。但是，基因顺序保守性差。隐藻mtDNA的特征包括类似于α-变形细菌操纵子的大型同义簇，其编码细菌样rRNA，tRNA和核糖体蛋白基因。隐藻线粒体基因组保留了在许多其他真核生物中发现的几乎所有基因，包括nad，sdh，cox，cob和atp基因，但sdh2和atp3除外。另外，基因簇分析表明，隐生植物具有与雅科比鞭毛虫雅科巴和雷克莫那氏菌非常相似的基因顺序。有趣的是，发现盐假单胞菌，两性拟南芥和Storeatula物种的cox1基因含有编码逆转录酶蛋白的II组内含子，而Storeatula物种CCMP1868的cob基因也是如此。这些新测序的基因组增加了可从藻类获得的数据的范围，并将有助于鉴定线粒体基因组进化的一般趋势。尽管大多数基因组是高度保守的，但广泛的基因排列已改变了基因顺序，这可能是由于与含发夹的移动遗传元件，回文序列的tRNA和串联重复序列相关的基因组重排。 cox1和cob基因序列表明内含子最近在隐生植物进化过程中获得。基于质体和线粒体基因组数据集的系统进化树的比较强调了当今隐生植物的宿主和共生体组分的不同进化历史。

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