Kim Eunsoo, Lane Christopher E, Curtis Bruce A, Kozera Catherine, Bowman Sharen, Archibald John M
Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
BMC Genomics. 2008 May 12;9:215. doi: 10.1186/1471-2164-9-215.
Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes-a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented.
The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a approximately 20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22-336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages.
Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.
隐藻是一类神秘的单细胞真核生物，其质体通过二次（即真核生物 - 真核生物）内共生获得。隐藻不同寻常之处在于它们拥有四个基因组——一个源自宿主细胞的核基因组和线粒体基因组，以及一个源自内共生体的质体基因组和“核质体”基因组。目前，对于隐藻藻类宿主和内共生体成分的进化起源了解甚少。到目前为止，仅测定了隐藻盐生红胞藻的单个完整线粒体基因组序列。在此，我们展示了隐藻藻类安徒生半隐藻CCMP644的第二个完整线粒体基因组。
安徒生半隐藻的线粒体DNA（mtDNA）大小为60,553 bp，编码30个结构RNA和36个蛋白质编码基因，所有基因都位于同一条链上。该基因组的一个显著特征是存在一个约20 Kbp长的基因间隔区，由众多22 - 336 bp的串联和分散重复单元组成。在这些重复序列附近有27个回文序列拷贝，预计可形成稳定的DNA茎环结构。其中一个这样的茎环位于富含GC和贫GC区域附近，可能在复制或转录中具有调控功能。安徒生半隐藻的mtDNA与盐生红胞藻的基因组有许多共同特征，包括总体结构、基因内容以及存在一个大的重复区域。然而，安徒生半隐藻的mtDNA没有反向重复序列和内含子，而盐生红胞藻中存在这些序列。对两个基因组中编码的tRNA套件进行比较分析表明，安徒生半隐藻的mtDNA已经丢失或转化了其原始的trnK(uuu)基因，并拥有一个源自trnS的“trnK(uuu)”，它似乎无法产生功能性tRNA。线粒体蛋白质编码基因系统发育强烈支持各种先前确立的真核生物类群，但未能解析高阶真核生物谱系之间的关系。
安徒生半隐藻和盐生红胞藻线粒体基因组的比较揭示了一些隐藻特有的基因组特征，最显著的是存在一个富含重复序列的大基因间隔区。然而，与盐生红胞藻不同，安徒生半隐藻的mtDNA不具有内含子且缺乏赖氨酸tRNA，推测该tRNA是从细胞质中导入的。
