Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae).
Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae).
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DOI：
10.1186/s12862-015-0544-5
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发表时间：
2015-12-01
影响因子：
3.4
通讯作者：
Turmel M
中科院分区：
文献类型：
--
作者：
Lemieux C;Vincent AT;Labarre A;Otis C;Turmel M
绿藻纲（绿藻门）包括形态和生态多样的绿藻。大多数已记录的物种属于由衣藻目（也称为团藻目）和球藻目形成的分支。尽管基于核18S rRNA基因或少数几个组合基因的研究已经阐明了衣藻目的多样性和系统发育结构，但许多已确定的单系群的位置仍然不确定。在此，我们使用叶绿体系统基因组学方法来描绘这些谱系之间的关系。
为了生成用于分析的氨基酸和核苷酸数据集，我们对24种绿藻纲分类群的叶绿体DNA（cpDNA）进行了测序；其中包括先前在衣藻目中确认的21个主要分支中的16个的代表，来自一个疑似与戈登金藻科为姐妹群的球藻状谱系（杰努法属）的两个分类群，以及两个球藻目物种。使用贝叶斯和/或最大似然推断方法，我们分析了一个由73种核心绿藻（包括33种绿藻纲物种）的69种cpDNA编码蛋白质组装而成的氨基酸数据集，以及两个由编码这些蛋白质的69个基因和29个RNA编码基因生成的核苷酸数据集。蛋白质和基因系统发育树是一致的，并且稳健地解析了大多数所研究谱系的分支顺序。在衣藻目中，22个分类群形成了由五个主要分支/谱系组成的集合。最早分化的分支包含平滑哈夫尼藻和十字卡特藻，其次是辐射卡特藻，然后是绿藻藻属。后者的谱系是两个超分支的姐妹群，一个由卵配衣藻属和莱因哈德衣藻属组成，另一个由尾团藻属和异团藻属组成。令我们惊讶的是，杰努法属物种以及属于戈登金藻属和特鲁巴藻属的两种具刺绿藻被归在一个具有高度支持的单系群中，该群还包括代表球藻目不同科（刚毛藻科、微芒藻科和栅藻科）的三个分类群。
我们的系统基因组学研究增进了我们对衣藻目界定和内部结构的了解，表明一个先前未被识别的谱系是球藻目的姐妹群。此外，它为衣藻目和球藻目创始成员的鞭毛结构提供了新的见解。
本文的在线版本（doi:10.1186/s12862 - 015 - 0544 - 5）包含补充材料，授权用户可获取。
The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis and the Crucicarteria, and was followed by the Radicarteria and then by the Chloromonadinia. The latter lineage was sister to two superclades, one consisting of the Oogamochlamydinia and Reinhardtinia and the other of the Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the two spine-bearing green algae belonging to the Golenkinia and Treubaria genera were recovered in a highly supported monophyletic group that also included three taxa representing distinct families of the Sphaeropleales (Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae). Our phylogenomic study advances our knowledge regarding the circumscription and internal structure of the Chlamydomonadales, suggesting that a previously unrecognized lineage is sister to the Sphaeropleales. In addition, it offers new insights into the flagellar structures of the founding members of both the Chlamydomonadales and Sphaeropleales. The online version of this article (doi:10.1186/s12862-015-0544-5) contains supplementary material, which is available to authorized users.