Research Topics
| J Peter GogartenSummaryAffiliation: University of Connecticut Country: USA Publications
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Detail Information
Publications
Quartet decomposition server: a platform for analyzing phylogenetic treesFenglou Mao
Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green St, Athens, GA 30622, USA
BMC Bioinformatics 13:123. 2012..This approach was shown to be useful in several studies of completely sequenced microbial genomes...- Visualization of the phylogenetic content of five genomes using dekapentagonal mapsOlga Zhaxybayeva
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA
Genome Biol 5:R20. 2004..Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods... - Concerted gene recruitment in early plant evolutionJinling Huang
Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
Genome Biol 9:R109. 2008..However, no systematic studies on the scope of anciently acquired genes and their impact on macroevolution are currently available in eukaryotes... - Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?Jinling Huang
Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
Genome Biol 8:R99. 2007..This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria... - Prokaryotic evolution and the tree of life are two different thingsEric Bapteste
UPMC, UMR CNRS 7138, 75005 Paris, France
Biol Direct 4:34. 2009..In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution... - Home and away- the evolutionary dynamics of homing endonucleasesAdi Barzel
Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
BMC Evol Biol 11:324. 2011.... - A hybrid clustering approach to recognition of protein families in 114 microbial genomesTimothy J Harlow
Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
BMC Bioinformatics 5:45. 2004..g. as the result of matches to so-called promiscuous domains. Use of the Markov Cluster algorithm avoids this non-specificity, but does not preserve topological or threshold information about protein families... - PentaPlot: a software tool for the illustration of genome mosaicismLutz Hamel
Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI 02881, USA
BMC Bioinformatics 6:139. 2005..PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix... - The intein of the Thermoplasma A-ATPase A subunit: structure, evolution and expression in E. coliA G Senejani
Department of Molecular and Cell Biology, University of Connecticut, 75 North Eagleville Rd Storrs, CT 06269 3044, USA
BMC Biochem 2:13. 2001..In addition to this splicing activity, most reported inteins also contain an endonuclease domain that is important in intein propagation... 
Gene transfer: gene swapping craze reaches eukaryotesJ Peter Gogarten
Department of Molecular Biology, University of Connecticut, 75 North Eagleville Road, Storrs, 06269 3044, Connecticut, USA
Curr Biol 13:R53-4. 2003..The mechanisms and frequencies of these transfers remain the subject of speculation, but the findings provide ample reason to seriously consider interspecies gene transfer as an important evolutionary process in eukaryotes...- Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elementsJ Peter Gogarten
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 31258, USA
BMC Evol Biol 6:94. 2006..BMC Evol Biol 2006, 6:42) provide important stepping stones towards integrated studies on how these parasitic elements evolve through time together with, or despite, their hosts... - Inteins: structure, function, and evolutionJ Peter Gogarten
Department of Molecular and Cell Biology, University of Connecticut, 75 North Eagleville Road, Storrs 06269 3044, USA
Annu Rev Microbiol 56:263-87. 2002..In particular, this review considers inteins as selfish or parasitic genetic elements, a point of view that explains many otherwise puzzling aspects of inteins... - Horizontal gene transfer, genome innovation and evolutionJ Peter Gogarten
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 3125, USA
Nat Rev Microbiol 3:679-87. 2005.... - A rooted net of lifeDavid Williams
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
Biol Direct 6:45. 2011..Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages... - Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the AzoresKristen S Swithers
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 3125, USA
J Bacteriol 193:5869-70. 2011..This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales... - Genome mosaicism and organismal lineagesOlga Zhaxybayeva
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
Trends Genet 20:254-60. 2004 - Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elementsKristen S Swithers
Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
BMC Evol Biol 9:303. 2009..Here we provide quantitative statistical support from an analyses of proteins that host inteins, group I introns, group II introns and spliceosomal introns across all three domains of life... 
Rooting the ribosomal tree of lifeGregory P Fournier
Department of Molecular and Cell Biology, University of Connecticut, CT, USA
Mol Biol Evol 27:1792-801. 2010....- Filling the gaps in the genomic landscapeDavid Williams
Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
Genome Biol 11:103. 2010..A new initiative provides comparative genomicists with a more complete picture of genome diversity. Here we discuss the improved sampling strategy... - Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the ThermotogalesKristen S Swithers
Department of Molecular and Cell Biology, University of Connecticut, CT, USA
Genome Biol Evol 4:730-9. 2012..Genes in T. africanus with apparent B(12) riboswitches were found to be down-regulated in the presence of vitamin B(12) consistent with their roles in B(12) synthesis and cobinamide salvage... - Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologsAmanda K Petrus
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
PLoS ONE 7:e40236. 2012..These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath... - Cladogenesis, coalescence and the evolution of the three domains of lifeOlga Zhaxybayeva
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
Trends Genet 20:182-7. 2004..Each contemporary molecule has its own history that traces back to an individual molecular cenancestor. However, these molecular ancestors were likely to be present in different organisms and at different times... - Biased gene transfer and its implications for the concept of lineageCheryl P Andam
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
Biol Direct 6:47. 2011..In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct... - BranchClust: a phylogenetic algorithm for selecting gene familiesMaria S Poptsova
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
BMC Bioinformatics 8:120. 2007.... - Using comparative genome analysis to identify problems in annotated microbial genomesMaria S Poptsova
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
Microbiology 156:1909-17. 2010..Researchers need to be aware of the existing errors in the annotation of even well-studied genomes, such as Escherichia coli, and consider additional quality control for their results... - Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of lifeGregory P Fournier
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 31258, USA
Philos Trans R Soc Lond B Biol Sci 364:2229-39. 2009..Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history... - Ancient gene duplications and the root(s) of the tree of lifeOlga Zhaxybayeva
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-31258, USA
Protoplasma 227:53-64. 2005.... - Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteriaKristen S Swithers
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
PLoS ONE 6:e23774. 2011..We conclude that the signal detected in James Lake's analysis in part results from a systematic artifact due to group size and diversity combined with low levels of horizontal gene transfer... - Trees in the web of lifeKristen S Swithers
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
J Biol 8:54. 2009.... - The power of phylogenetic approaches to detect horizontally transferred genesMaria S Poptsova
Department of Molecular and Cell Biology, University of Connecticut, CT, USA
BMC Evol Biol 7:45. 2007..Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods?.. - Spliceosomal introns: new insights into their evolutionOlga Zhaxybayeva
Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125, USA
Curr Biol 13:R764-6. 2003..Only a small subset of the analyzed introns was present in the common ancestor of plants, fungi, animals and Plasmodium... - Estimating the size of the bacterial pan-genomePascal Lapierre
University of Connecticut Biotechnology Center, 91 North Eagleville Road, Storrs, CT 06269 3149, USA
Trends Genet 25:107-10. 2009..Our findings indicate that the pan-genome of the bacterial domain is of infinite size (the Bacteria as a whole have an open pan-genome) and that approximately 250 genes per genome belong to the extended bacterial core genome... - Evolution of mal ABC transporter operons in the Thermococcales and ThermotogalesKenneth M Noll
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
BMC Evol Biol 8:7. 2008..We examined deep phylogenetic relationships among the mal genes of these hyperthermophiles and their close relatives to look for evidence of shared ancestry... - Biased gene transfer mimics patterns created through shared ancestryCheryl P Andam
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
Proc Natl Acad Sci U S A 107:10679-84. 2010..We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer... - An improved probability mapping approach to assess genome mosaicismOlga Zhaxybayeva
Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
BMC Genomics 4:37. 2003..Here we extend the probability mapping approach by improving taxon sampling of the analyzed datasets, and by using bootstrap support values, a more conservative tool to assess reliability... - Biased gene transfer in microbial evolutionCheryl P Andam
Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269 3125, USA
Nat Rev Microbiol 9:543-55. 2011..We also discuss the role of biased gene transfer in the formation of taxonomically recognizable natural groups in the tree or net of life... - Inferring the ancient history of the translation machinery and genetic code via recapitulation of ribosomal subunit assembly ordersGregory P Fournier
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
PLoS ONE 5:e9437. 2010..Furthermore, we find that this ordering produces several trends in specific amino acid usages compatible with models of genetic code evolution... - Structural stability and endonuclease activity of a PI-SceI GFP-fusion proteinAlireza G Senejani
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
Int J Biol Sci 3:205-11. 2007..However, the endonuclease activity of the newly engineered protein was different from the wild-type protein in that it required the presence of Mn(2+) and not Mg(2+) metal cations for activity... - Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic ClostridiaGregory P Fournier
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 31258, USA
J Bacteriol 190:1124-7. 2008..This event likely occurred within the last 475 million years, causing profound changes in planetary methane biogeochemistry... - Ancient origin of the divergent forms of leucyl-tRNA synthetases in the HalobacterialesCheryl P Andam
Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Rd, Storrs, CT 06269 3125, USA
BMC Evol Biol 12:85. 2012..During the course of evolution, HGT has played an essential role in the origin and dissemination of genetic and metabolic novelty... - Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related speciesPascal Lapierre
Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT 06269-3125, USA
Syst Appl Microbiol 29:15-23. 2006..For all the Thermus and Deinococcus species surveyed, including Thermus scotoductus, cultures that were free of contamination only contained an A/V-type ATP synthases... - Prokaryotic evolution in light of gene transferJ Peter Gogarten
Department of Molecular and Cell Biology, University of Connecticut, CT, USA
Mol Biol Evol 19:2226-38. 2002.... - Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence dataAdam C Silver
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
PLoS ONE 6:e16751. 2011..Instead, the detection of genes critical in the adaptation to specific niches may help to reveal the physiological specialization of these strains... - Quantifying Homologous Replacement of Loci between Haloarchaeal SpeciesDavid Williams
Department of Molecular and Cell Biology, University of Connecticut
Genome Biol Evol 4:1223-44. 2012.... - Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North SeaKristen S Swithers
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
J Bacteriol 193:5566-7. 2011..Its genome sequence reveals extensive gene gains and a large content of mobile genetic elements. It also contains putative hydrogenase genes that have no homologs in the other member of the Thermotogales... - Signature of a primitive genetic code in ancient protein lineagesGregory P Fournier
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
J Mol Evol 65:425-36. 2007..Thus, expansion of the genetic code likely set the stage for the transition from RNA-based to protein-based life... - The role of reticulate evolution in creating innovation and complexityKristen S Swithers
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
Int J Evol Biol 2012:418964. 2012..We discuss how these different evolutionary processes contribute to generating innovation and complexity... - Whole-genome analysis of photosynthetic prokaryotesJason Raymond
Department of Chemistry and Biochemistry, Arizona State University (ASU, Tempe, AZ 85287-1604, USA
Science 298:1616-20. 2002..Our results explain incoherencies in previous data-limited phylogenetic analyses of phototrophic bacteria and indicate that the core components of photosynthesis have been subject to lateral transfer... - Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approachJason Raymond
Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
Philos Trans R Soc Lond B Biol Sci 358:223-30. 2003..A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared... - A hyperconserved protein in Prochlorococcus and marine SynechococcusOlga Zhaxybayeva
Department of Biochemistry and Molecular Biology, Dalhousie University, NS, Canada
FEMS Microbiol Lett 274:30-4. 2007..Comparative analyses indicate that the hyperconserved protein, which may be involved in interactions with nucleic acids, is under stabilizing selection and has resided in these genomes since the last common ancestor of the group... - Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strainsAlessia Morandi
Institute for Infectious Diseases, University of Berne, Switzerland
J Bacteriol 187:6561-4. 2005..5%. The SSU copies from Aeromonas veronii LMG13695 clustered with sequences from four Aeromonas species. These results demonstrate intragenomic heterogeneity of SSU and suggest caution when using SSU to identify aeromonads... - Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer eventsOlga Zhaxybayeva
Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
Genome Res 16:1099-108. 2006..However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases... - The evolution of eukaryotesWilliam Martin
Science 316:542-3; author reply 542-3. 2007 - Were arachnids the first to use combinatorial peptide libraries?Brianna L Sollod
Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06032 3305, USA
Peptides 26:131-9. 2005..This gene-based combinatorial peptide library strategy appears to have been first implemented by arachnids almost 400 million years ago, long before cone snails evolved a similar mechanism for generating peptide diversity...