Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions.
Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions.
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DOI：
10.1093/molbev/msq200
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发表时间：
2011
影响因子：
10.7
通讯作者：
Daniel J. G. Lahr;Truc B Nguyen;E. Barbero;Laura A. Katz
中科院分区：
文献类型：
--
作者：
Daniel J. G. Lahr;Truc B Nguyen;E. Barbero;Laura A. Katz
肌动蛋白基因家族的进化特征是在真核生物的生命树中独立的扩张和收缩。在这里，我们评估肌动蛋白基因序列的多样性在三个谱系的属Arcella，一个自由生活的有遗嘱（带壳）变形虫在Arcellinida。建立了两个形态种的四个无性系：Arcella hemisphaerica和A. vulgaris，并利用小亚基核糖体DNA（SSU-rDNA）系谱分析了它们在“阿米巴虫”内的系统发育关系。我们确定A. hemisphaerica和A.寻常型是独立的遗传谱系。此外，我们的特点是多个肌动蛋白基因拷贝从所有的血统。分析所得到的序列揭示了许多不同的肌动蛋白基因，其主要不同的同义替换。我们估计肌动蛋白基因家族在每个谱系中包含40-50个旁系同源成员。三个独立的谱系中没有一个与另一个共享相同的同源性，肌动蛋白之间的分歧达到29%，而SSU-rDNA仅为2%。有效密码子数（ENC），成分偏差，重组签名，和遗传多样性的背景下的基因树的分析表明，有两组肌动蛋白进化与不同的分子进化模式。在这些群体中，肌动蛋白基因在每个谱系中都有多个独立的扩增。总之，这些数据表明，这两个群体位于Arcella基因组的不同区域。此外，我们比较了Arcella肌动蛋白基因家族与黏菌Dictyosteelium discoideum和变形虫分支的其他成员中相对较好描述的基因家族。在Arcella和Dictyosteelium中分子进化的总体模式是相似的。然而，分离的基因在两个不同的群体加上最近的扩张是Arcella的特点，并可能反映了一个不寻常的模式的基因家族进化的叶状有遗嘱阿米巴。我们提供了一个模型来解释两个不同的群体的存在和最近的独立扩张导致大量的肌动蛋白在每个血统的模式。
The evolution of actin gene families is characterized by independent expansions and contractions across the eukaryotic tree of life. Here, we assess diversity of actin gene sequences within three lineages of the genus Arcella, a free-living testate (shelled) amoeba in the Arcellinida. We established four clonal lines of two morphospecies, Arcella hemisphaerica and A. vulgaris, and assessed their phylogenetic relationship within the "Amoebozoa" using small subunit ribosomal DNA (SSU-rDNA) genealogy. We determined that the two lines of A. hemisphaerica are identical in SSU-rDNA, while the two A. vulgaris are independent genetic lineages. Furthermore, we characterized multiple actin gene copies from all lineages. Analyses of the resulting sequences reveal numerous diverse actin genes, which differ mostly by synonymous substitutions. We estimate that the actin gene family contains 40-50 paralogous members in each lineage. None of the three independent lineages share the same paralog with another, and divergence between actins reaches 29% in contrast to just 2% in SSU-rDNA. Analyses of effective number of codons (ENC), compositional bias, recombination signatures, and genetic diversity in the context of a gene tree indicate that there are two groups of actins evolving with distinct patterns of molecular evolution. Within these groups, there have been multiple independent expansions of actin genes within each lineage. Together, these data suggest that the two groups are located in different regions of the Arcella genome. Furthermore, we compare the Arcella actin gene family with the relatively well-described gene family in the slime mold Dictyostelium discoideum and other members of the Amoebozoa clade. Overall patterns of molecular evolution are similar in Arcella and Dictyostelium. However, the separation of genes in two distinct groups coupled with recent expansion is characteristic of Arcella and might reflect an unusual pattern of gene family evolution in the lobose testate amoebae. We provide a model to account for both the existence of two distinct groups and the pattern of recent independent expansion leading to a large number of actins in each lineage.