Khan Hameed, Parks Natalie, Kozera Catherine, Curtis Bruce A, Parsons Byron J, Bowman Sharen, Archibald John M
Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
Mol Biol Evol. 2007 Aug;24(8):1832-42. doi: 10.1093/molbev/msm101. Epub 2007 May 23.
Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red algal plastids independent of those in heterokont, haptophyte, and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns, and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a noncyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte, and cryptophyte (i.e., chromist) plastids were monophyletic, and heterokonts and haptophytes were each other's closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.
隐藻是一类单细胞藻类，具有含叶绿素c的质体，这些质体源自对次级（即真核）内共生体的摄取。生化和分子数据表明，隐藻质体源自红藻，但隐藻获取其红藻质体是否独立于不等鞭毛类、定鞭藻和甲藻的质体这一问题长期以来一直存在争议。为了更好地理解隐藻质体的起源和进化，我们对盐生红胞藻CCMP1319的质体基因组进行了测序：其长度为135,854 bp，是迄今为止所表征的最大的次级质体基因组。它还具有在亲缘关系较远的隐藻古氏巴夫藻或其他红藻次级质体中未见的有趣特征，包括假基因、内含子，以及一个源自细菌的DNA聚合酶III（dnaX）的tau/γ亚基基因，这是首次在任何质体基因组中发现推定的DNA复制机制。系统发育分析表明，dnaX是在红胞藻的一个祖先中通过横向基因转移（LGT）获得的，最有可能来自厚壁菌门细菌。全基因组调查显示，除了一个类似于最近在其他隐藻和定鞭藻中表征的非蓝细菌型rpl36基因外，没有其他LGT的情况。对15个完整质体基因组中编码的45种蛋白质进行严格的串联分析，得到的系统发育树中，不等鞭毛类、定鞭藻和隐藻（即色藻）的质体是单系的，不等鞭毛类和定鞭藻是彼此最亲近的亲属。然而，当根据氨基酸的化学性质重新编码以尽量减少组成偏差的影响时，对色藻单系性的统计支持消失了，并且串联分析的很大一部分似乎与隐藻和定鞭藻质体之间的姐妹群关系一致。
