Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites

Chen, 2013, New genes as drivers of phenotypic evolution, Nat Rev Genet, 14, 645, 10.1038/nrg3521 Skippington, 2011, Lateral genetic transfer and the construction of genetic exchange communities, FEMS Microbiol Rev, 35, 707, 10.1111/j.1574-6976.2010.00261.x Zhaxybayeva, 2011, Lateral gene transfer, Curr Biol, 21, R242, 10.1016/j.cub.2011.01.045 Andersson, 2009, Gene transfer and diversification of microbial eukaryotes, Annu Rev Microbiol, 63, 177, 10.1146/annurev.micro.091208.073203 Keeling, 2009, Functional and ecological impacts of horizontal gene transfer in eukaryotes, Curr Opin Genet Dev, 19, 613, 10.1016/j.gde.2009.10.001 Williams, 2013, An archaeal origin of eukaryotes supports only two primary domains of life, Nature, 504, 231, 10.1038/nature12779 Timmis, 2004, Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes, Nat Rev Genet, 5, 123, 10.1038/nrg1271 McFadden, 2014, Origin and evolution of plastids and photosynthesis in eukaryotes, Cold Spring Harb Perspect Biol, 6, a016105, 10.1101/cshperspect.a016105 Feschotte, 2012, Endogenous viruses: insights into viral evolution and impact on host biology, Nat Rev Genet, 13, 283, 10.1038/nrg3199 Wallau, 2012, Horizontal transposon transfer in eukarya: detection, bias, and perspectives, Genome Biol Evol, 4, 689, 10.1093/gbe/evs055 Alvarez-Ponce, 2013, Gene similarity networks provide tools for understanding eukaryote origins and evolution, Proc Natl Acad Sci U S A, 110, E1594, 10.1073/pnas.1211371110 Alsmark, 2013, Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes, Genome Biol, 14, R19, 10.1186/gb-2013-14-2-r19 Weiser, 2011 Soanes, 2014, Horizontal gene transfer in eukaryotic plant pathogens, Annu Rev Phytopathol, 52, 583, 10.1146/annurev-phyto-102313-050127 Adl, 2012, The revised classification of eukaryotes, J Eukaryot Microbiol, 59, 429, 10.1111/j.1550-7408.2012.00644.x del Campo, 2014, The others: our biased perspective of eukaryotic genomes, Trends Ecol Evol, 29, 252, 10.1016/j.tree.2014.03.006 Clemente, 2012, The impact of the gut microbiota on human health: an integrative view, Cell, 148, 1258, 10.1016/j.cell.2012.01.035 Smillie, 2011, Ecology drives a global network of gene exchange connecting the human microbiome, Nature, 480, 241, 10.1038/nature10571 Langille, 2012, Human microbiome: a genetic bazaar for microbes?, Curr Biol, 22, R20, 10.1016/j.cub.2011.11.023 Cirimotich, 2011, Native microbiota shape insect vector competence for human pathogens, Cell Host Microbe, 10, 307, 10.1016/j.chom.2011.09.006 Popa, 2011, Trends and barriers to lateral gene transfer in prokaryotes, Curr Opin Microbiol, 14, 615, 10.1016/j.mib.2011.07.027 Vavra, 2013, Microsporidia and ‘the art of living together’, Adv Parasitol, 82, 253, 10.1016/B978-0-12-407706-5.00004-6 Grant, 2014, Phylogenomic study indicates widespread lateral gene transfer in Entamoeba and suggests a past intimate relationship with parabasalids, Genome Biol Evol, 10.1093/gbe/evu179 Strese, 2014, A recently transferred cluster of bacterial genes in Trichomonas vaginalis—lateral gene transfer and the fate of acquired genes, BMC Evol Biol, 14, 119, 10.1186/1471-2148-14-119 Brotman, 2012, Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women, Sex Transm Dis, 39, 807, 10.1097/OLQ.0b013e3182631c79 Maritz, 2014, What is the importance of zoonotic Trichomonads for human health?, Trends Parasitol, 30, 333, 10.1016/j.pt.2014.05.005 Jain, 1999, Horizontal gene transfer among genomes: the complexity hypothesis, Proc Natl Acad Sci U S A, 96, 3801, 10.1073/pnas.96.7.3801 Gould, 2013, Deep sequencing of Trichomonas vaginalis during the early infection of vaginal epithelial cells and amoeboid transition, Int J Parasitol, 43, 707, 10.1016/j.ijpara.2013.04.002 Huang, 2014, Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis, Biochim Biophys Acta, 1840, 53, 10.1016/j.bbagen.2013.08.008 Beiko, 2008, Detecting lateral genetic transfer: a phylogenetic approach, Methods Mol Biol, 452, 457, 10.1007/978-1-60327-159-2_21 Beiko, 2009, Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction, Methods Mol Biol, 532, 241, 10.1007/978-1-60327-853-9_14 Ragan, 2001, On surrogate methods for detecting lateral gene transfer, FEMS Microbiol Lett, 201, 187, 10.1111/j.1574-6968.2001.tb10755.x Chan, 2013, Next-generation phylogenomics, Biol Direct, 8, 3, 10.1186/1745-6150-8-3 Nakjang, 2012, A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes, PloS One, 7, e30287, 10.1371/journal.pone.0030287 Mallet, 2010, Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus, BMC Genomics, 11, 171, 10.1186/1471-2164-11-171 Thiergart, 2012, An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin, Genome Biol Evol, 4, 466, 10.1093/gbe/evs018 Choi, 2007, Global extent of horizontal gene transfer, Proc Natl Acad Sci U S A, 104, 4489, 10.1073/pnas.0611557104 Rochette, 2014, Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes, Mol Biol Evol, 31, 832, 10.1093/molbev/mst272 Schonknecht, 2014, Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution, Bioessays, 36, 9, 10.1002/bies.201300095 Huang, 2013, Horizontal gene transfer in eukaryotes: the weak-link model, Bioessays, 35, 868, 10.1002/bies.201300007 Boto, 2014, Horizontal gene transfer in the acquisition of novel traits by metazoans, Proc Biol Sci, 281, 20132450, 10.1098/rspb.2013.2450 Lill, 2009, Function and biogenesis of iron-sulphur proteins, Nature, 460, 831, 10.1038/nature08301 Nyvltova, 2013, NIF-type iron-sulfur cluster assembly system is duplicated and distributed in the mitochondria and cytosol of Mastigamoeba balamuthi, Proc Natl Acad Sci U S A, 110, 7371, 10.1073/pnas.1219590110 Stairs, 2014, A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist pygsuia, Curr Biol, 24, 1176, 10.1016/j.cub.2014.04.033 Jackson, 2008, Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa), BMC Genomics, 9, 594, 10.1186/1471-2164-9-594 Carlton, 2007, Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis, Science, 315, 207, 10.1126/science.1132894 Aurrecoechea, 2009, GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis, Nucleic Acids Res, 37, D526, 10.1093/nar/gkn631 Clarke, 2013, Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling, Genome Biol, 14, R11, 10.1186/gb-2013-14-2-r11