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    Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

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    Authors
    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 S
    Hutchins, Andrew P
    Weinmeier, Thomas
    Rattei, Thomas
    Chu, Jeffery SC
    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
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    Issue Date
    2013-02-01
    
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    Citation
    Genome Biology. 2013 Feb 01;14(2):R11
    URI
    http://dx.doi.org/10.1186/gb-2013-14-2-r11
    http://hdl.handle.net/10147/294458
    Abstract
    Abstract Background 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. Results 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. Conclusions 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.
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