Clarke Michael, Lohan Amanda J, Liu Bernard, Lagkouvardos Ilias, Roy Scott, Zafar Nikhat, Bertelli Claire, Schilde Christina, Kianianmomeni Arash, Bürglin Thomas R, Frech Christian, Turcotte Bernard, Kopec Klaus O, Synnott John M, Choo Caleb, Paponov Ivan, Finkler Aliza, Heng Tan Chris Soon, Hutchins Andrew P, Weinmeier Thomas, Rattei Thomas, Chu Jeffery S C, Gimenez Gregory, Irimia Manuel, Rigden Daniel J, Fitzpatrick David A, Lorenzo-Morales Jacob, Bateman Alex, Chiu Cheng-Hsun, Tang Petrus, Hegemann Peter, Fromm Hillel, Raoult Didier, Greub Gilbert, Miranda-Saavedra Diego, Chen Nansheng, Nash Piers, Ginger Michael L, Horn Matthias, Schaap Pauline, Caler Lis, Loftus Brendan J
Genome Biol. 2013 Feb 1;14(2):R11. doi: 10.1186/gb-2013-14-2-r11.
The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.
Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms.
Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.
变形虫门是真核生物的主要分支之一，包含具有生物医学和进化重要性的分类群，但其基因组多样性在很大程度上仍未得到充分采样。在此，我们展示了对卡氏棘阿米巴（Ac）全基因组组装的分析，Ac是首个来自独立自由生活变形虫的代表。
Ac编码15,455个内含子丰富的紧密基因，其中大量基因预计是通过跨界横向基因转移（LGT）产生的。大多数LGT候选基因经历了大量的内含子化过程，并且Ac似乎已将它们纳入已建立的转录程序中。Ac表现出复杂的信号传导和细胞通讯功能，包括完整的酪氨酸激酶信号传导工具包，以及与兼性多细胞盘基网柄菌中发现的预测细胞外受体相当的多样性。作为多种细菌和病毒的重要环境宿主，Ac利用了多种预测的模式识别受体，其中许多在高等生物的先天免疫系统中具有预测的直系同源功能。
我们的分析突出了LGT在Ac生物学以及微生物真核生物多样化中的重要作用。参与后生动物多细胞性进化的关键信号传导机制的早期进化有力地证明了其在单鞭毛类谱系早期的出现。总体而言，Ac基因组的可得性应有助于解读变形虫门的生物学特性，并促进对这种重要模式生物和环境宿主的功能基因组学研究。
