Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling
Mike Clarke,Amanda J. Lohan,Bernard A. Liu,Ilias Lagkouvardos,Scott William Roy,Nikhat Zafar,Claire Bertelli,Christina Schilde,Arash Kianianmomeni,Thomas R. Bürglin,Christian Frech,Bernard Turcotte,Klaus O. Kopec,John M. Synnott,Caleb Choo,Ivan A. Paponov,Aliza Finkler,Chris Soon Heng Tan,Andrew P. Hutchins,Thomas Weinmeier,Thomas Rattei,Jeffery Sc Chu,Gregory Gimenez,Manuel Irimia,Daniel J. Rigden,David A. Fitzpatrick,Jacob Lorenzo-Morales,Alex Bateman,Cheng-Hsun Chiu,Petrus Tang,Peter Hegemann,Hillel Fromm,Didier Raoult,Gilbert Greub,Diego Miranda-Saavedra,Nansheng Chen,Piers Nash,Michael L. Ginger,Matthias Horn,Pauline Schaap,Lis Caler,Brendan J. Loftus +41 more
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TLDR
In this paper, the authors present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary freeliving amoebozoan.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 freeliving 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.read more
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Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.
Nadège Philippe,Nadège Philippe,Matthieu Legendre,Gabriel Doutre,Yohann Couté,Olivier Poirot,Magali Lescot,Defne Arslan,Virginie Seltzer,Lionel Bertaux,Christophe Bruley,Jérôme Garin,Jean-Michel Claverie,Chantal Abergel +13 more
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An update on Acanthamoeba keratitis: diagnosis, pathogenesis and treatment
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Homeodomain proteins: an update.
TL;DR: An update of the review on homeobox genes that was written together with Walter Gehring in 1994 is provided, using the 103 Drosophila homeOBox genes as example, and an updated classification is presented.
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Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages
Alex de Mendoza,Arnau Sebé-Pedrós,Arnau Sebé-Pedrós,Martin Sebastijan Šestak,Marija Matejčić,Guifré Torruella,Guifré Torruella,Tomislav Domazet-Lošo,Iñaki Ruiz-Trillo,Iñaki Ruiz-Trillo,Iñaki Ruiz-Trillo +10 more
TL;DR: Using comparative genomics and expression data, the view on how TFs contributed to eukaryotic evolution is reshaped and the importance of TFs to the origins of multicellularity and embryonic development is revealed.
References
More filters
Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Journal ArticleDOI
Mechanisms of phagocytosis in macrophages
Alan Aderem,David M. Underhill +1 more
TL;DR: Macrophages also play an important role in the recognition and clearance of apoptotic cells; a notable feature of this process is the absence of an inflammatory response.
Journal ArticleDOI
Gene finding in novel genomes
TL;DR: The SNAP gene finder is introduced which has been designed to be easily adaptable to a variety of genomes and finds that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate.
Journal ArticleDOI
The origins of genome complexity.
Michael Lynch,John S. Conery +1 more
TL;DR: It is argued that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size, and provided novel substrates for the secondary evolution of phenotypic complexity by natural selection.
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