Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts.
Mol Biol Evol. 2011 Jan;28(1):223-36. doi: 10.1093/molbev/msq200. Epub 2010 Aug 2.
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.
肌动蛋白基因家族的进化特点是在真核生物进化树上独立扩张和收缩。在这里，我们评估了 Arcellinida 目中自由生活的有壳变形虫属 Arcella 内三个谱系的肌动蛋白基因序列的多样性。我们建立了两个形态种，Arcella hemisphaerica 和 A. vulgaris 的四个克隆系，并使用小亚基核糖体 DNA (SSU-rDNA) 系统发育评估了它们在 "变形虫" 中的系统发育关系。我们确定，这两个 A. hemisphaerica 系的 SSU-rDNA 完全相同，而两个 A. vulgaris 是独立的遗传谱系。此外，我们从所有谱系中鉴定了多个肌动蛋白基因拷贝。对所得序列的分析揭示了许多不同的肌动蛋白基因，它们主要通过同义替换而不同。我们估计，每个谱系的肌动蛋白基因家族包含 40-50 个直系同源物。这三个独立谱系中的任何一个都与另一个没有相同的直系同源物，而肌动蛋白之间的差异达到 29%，而 SSU-rDNA 仅为 2%。在基因树的背景下，对有效密码子数 (ENC)、组成偏倚、重组特征和遗传多样性的分析表明，有两组肌动蛋白以不同的分子进化模式进化。在这些组中，每个谱系内都有多个肌动蛋白基因的独立扩张。总的来说，这些数据表明这两组位于 Arcella 基因组的不同区域。此外，我们将 Arcella 肌动蛋白基因家族与相对描述良好的粘菌 Dictyostelium discoideum 基因家族以及 Amoebozoa 进化枝的其他成员进行了比较。Arcella 和 Dictyostelium 的分子进化总体模式相似。然而，两组基因的分离以及最近的扩张是 Arcella 的特征，可能反映了有壳变形虫中基因家族进化的一种不寻常模式。我们提供了一个模型来解释两组的存在以及最近独立扩张导致每个谱系中大量肌动蛋白的模式。
