Phylogenomic Analysis of Kinetoplastids Supports That Trypanosomatids Arose from within Bodonids
Phylogenomic Analysis of Kinetoplastids Supports That Trypanosomatids Arose from within Bodonids
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DOI：
10.1093/molbev/msq289
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发表时间：
2011-01-01
影响因子：
10.7
通讯作者：
Moreira, David
中科院分区：
文献类型：
--
作者：
Deschamps, Philippe;Lara, Enrique;Moreira, David
着丝质体是一大群自由生活和寄生的真核鞭毛虫，包括医学上重要的锥虫（如锥虫和利什曼原虫）和广泛存在的自由生活和寄生的骨线虫。基于小亚基rRNA和保守蛋白的系统发育支持着丝体分为五个目（原动质体、新体、副体、真体和锥虫体），但它们产生的相对分支顺序不一致，尤其是锥虫体的位置。一般来说，小亚基rRNA倾向于支持它们的早期出现，而蛋白质系统发育通常支持更近的起源。为了通过系统基因组学方法解决这一问题，我们对三个齿形目（Bodo saltans - eubodonida -， Procryptobia sorokini - parabodonida -和Rhynchomonas nasuta - neobodonida -）的代表进行了大量的cDNA平行测序。我们鉴定了这些物种、4种锥虫和2种密切相关的外群物种（Euglena gracilis和Diplonema papillatum）共有的64种保守蛋白。系统发育分析的串联数据集产生了一个强有力的支持树显示晚出现的锥虫作为真虫纲的姐妹组。此外，我们在三种牙体物种中鉴定了参与锥虫体线粒体mRNA编辑的同源蛋白，这表明编辑可能在着丝质体中广泛存在。线粒体基因表达序列的比较显示，在U位置存在变异，这与与锥虫最密切相关的三个齿形目（新齿形目、副齿形目和真齿形目）存在编辑活性相一致。线粒体mRNA编辑似乎是着丝质体中一种古老的现象。
Kinetoplastids are a large group of free-living and parasitic eukaryotic flagellates, including the medically important trypanosomatids (e.g., Trypanosoma and Leishmania) and the widespread free-living and parasitic bodonids. Small subunit rRNA- and conserved protein-based phylogenies support the division of kinetoplastids into five orders (Prokinetoplastida, Neobodonida, Parabodonida, Eubodonida, and Trypanosomatida), but they produce incongruent results regarding their relative branching order, in particular for the position of the Trypanosomatida. In general, small subunit rRNA tends to support their early emergence, whereas protein phylogenies most often support a more recent origin from within bodonids. In order to resolve this question through a phylogenomic approach, we carried out massive parallel sequencing of cDNA from representatives of three bodonid orders (Bodo saltans -Eubodonida-, Procryptobia sorokini -Parabodonida-, and Rhynchomonas nasuta -Neobodonida-). We identified 64 well-conserved proteins shared by these species, four trypanosomatids, and two closely related outgroup species (Euglena gracilis and Diplonema papillatum). Phylogenetic analysis of a concatenated data set yielded a strongly supported tree showing the late emergence of trypanosomatids as a sister group of the Eubodonida. In addition, we identified homologues of proteins involved in trypanosomatid mitochondrial mRNA editing in the three bodonid species, suggesting that editing may be widespread in kinetoplastids. Comparison of expressed sequences from mitochondrial genes showed variability at U positions, in agreement with the existence of editing activity in the three bodonid orders most closely related to trypanosomatids (Neobodonida, Parabodonida, and Eubodonida). Mitochondrial mRNA editing appears to be an ancient phenomenon in kinetoplastids.