Peter Gogarten

Board of Trustees Distinguished Professor

Molecular and Cell Biology / Microbiology

Education: Ph.D. University of Giessen, FRG; Postdoctoral study, University of California Santa Cruz.

Research Interests: Molecular evolution; origin and early evolution of cellular life; evolution of the eukaryotic endomembrane system; horizontal gene transfer and gene duplications; comparative genome analyses; inteins, molecular parasites, and levels of selection.

Selected Publications:
[A complete list of publication including links to online versions is at http://gogarten.uconn.edu ]

• Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP (2021): The Evolutionary Origins of Extreme Halophilic Archaeal Lineages.  Genome Biology and Evolution 13 (8)   https://doi.org/10.1093/gbe/evab166
• Makkay AM, Louyakis AS, Ram‐Mohan N, Gophna U, Gogarten JP, Papke T (2020) Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon. Sci Rep 10,22297 (2020). https://doi.org/10.1038/s41598-020-79296-w
• Melnik TN, Papke RT, Gogarten JP, Kireev II, Surin AK, Beznosov SN, Galeva AV, Fedorov OV (2020) Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum. MicrobiologyOpen. 2020; 9:e1047. https://doi.org/10.1002/mbo3.1047
• Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S (2018) Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire. ISME J. 2018 Jun 28. doi 10.1038/s41396-018-0166-1.
• Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT (2018) Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing. Gene- Section: Microbial Genetics and Genomics, Genetic and Genomics Extremophiles 9(3), 129; doi: 10.3390/genes9030129.
• Shalev Y, Soucy SM, Papke RT, Gogarten JP, Eichler J, Gophna U (2018) Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax. Gene- Section: Microbial Genetics and Genomics, Genetic and Genomics Extremophiles9 (3), 172; https://doi.org/10.3390/genes9030172.
• Soucy SM, Gogarten JP (2017) Inteins as Indicators of Bio-Communication. Biocommunication of Archaea, 265-275, doi: 10.1007/978-3-319-65536-9_16.
• Dick AA, Harlow TJ, Gogarten JP (2017) Short branches lead to systematic artifacts when BLAST searches are used as surrogate for phylogenetic reconstruction. Mol Phylogenet 107:338-344. doi: 10.1016/j.ympev.2016.11.016. [Epub ahead of print]
• Omer S, Harlow TJ, GogartenJP (2017) Does Sequence Conservation Provide Evidence for Biological Function? Trends in Microbiology 25(1):11-18, doi: 10.1016/j.tim.2016.09.010
• Gogarten JP , Deamer D (2016) Is LUCA a thermophilic progenote? Nature Microbiology 1, 16229; doi: 10.1038/nmicrobiol.2016.229
• Adit Naor, Neta Altman-Price, Shannon M. Soucy, Anna G. Green (UConn undergrad), Yulia Mitiagin, Israela Turgeman-Grott, Noam Davidovich, Johann Peter Gogarten*, Uri Gophna*  (2016).
  Impact of a homing intein on recombination frequency and organismal fitness.
  PNAS 2016; published ahead of print July 26, 2016, doi:10.1073/pnas.1606416113
• Fournier G, Andam CP, Gogarten JP (2015) Ancient horizontal gene transfer and the last common ancestors. BMC Evolutionary Biology 15 (1) p. 70 doi: 10.1186/s12862-015-0350-0.
• Colston#, S., M. Fullmer#, L. Beka, B. Lamy, J. P. Gogarten*, J. Graf*. 2014.
  Evaluation of Bioinformatic Genome Comparisons for Taxonomic and Phylogenic Assignments using Aeromonas as a Test Case. #Co-first authors, *Co-corresponding authors.
  mBio doi:10.1128/mBio.02136-14
• Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT:
  Population and genomic analysis of the genus Halorubrum.
  Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140
• Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP and Papke RT (2014)
  Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations.
  Front. Microbiol. 5:143. doi: 10.3389/fmicb.2014.00143
• Lapierre P, Lasek-Nesselquist E, and Gogarten JP (2012) The impact of HGT on phylogenomic reconstruction methods Brief Bioinform [first published online August 20, 2012] doi:10.1093/bib/bbs050 [Fulltext]
• Swithers KS, Soucy SM, Gogarten JP (2012) The Role of Reticulate Evolution in Creating Innovation and Complexity. International Journal of Evolutionary Biology 2012, ID 418964, 10 pages, doi: 10.1155/2012/418964
• Fournier GP, Andam CP, Alm EJ, Gogarten JP (2012) Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life. Origins of Life and Evolution of Biospheres 41:621–632 [Pre-proof version] doi: 10.1007/s11084-011-9261-2
• Andam CP, Gogarten JP (2011) Biased gene transfer in microbial evolution. Nature Reviews in Microbiology 9(7): 543-555 , doi:10.1038/nrmicro2593 pubmed
• Cheryl P. Andam, David Williams, and J. Peter Gogarten (2010) Biased gene transfer mimics patterns created through shared ancestry.
  PNAS 107(23):10679-84 [Epub 2010 May 21] doi:10.1073/pnas.1001418107
  Reviewed by Yuri Wolf as a “Must Read” on Faculty of 1000 Fournier GP, Gogarten JP (2010) Rooting the Ribosomal Tree of Life. Molecular Biology and Evolution (Epub ahead of print)
• Swithers KS, Senejani AG, Fournier GP, Gogarten JP (2009)
  Conservation of intron and intein insertion sites: Implications for life histories of parasitic genetic elements.
  BMC Evolutionary Biology 2009, 9:303 doi:10.1186/1471-2148-9-303
• Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009)
  Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus 
  Genome Biology and Evolution: doi:10.1093/gbe/evp032
• Fournier GP, Huang JL, Gogarten JP (2009)
  Horizontal gene transfer from extinct and extant lineages: Biological innovation and the coral of life.
  Philos Trans R Soc Lond B Biol Sci. 364 (1527):2229-39.
• Maria B. Gogarten, Johann Peter Gogarten, Lorraine C. Olendzenski (Editors)
  Horizontal Gene Transfer: Genomes in Flux.
  Humana Press – Springer; 1 edition (February 13, 2009), ISBN-13: 978-1603278522
• Lapierre P., Gogarten J.P. (2009)
  Estimating the size of the bacterial pan-genome.
  Trends in Genetics, doi:10.1016/j.tig.2008.12.004
• Xu, Ying and J Peter Gogarten (eds.) (2008)
  Computational Methods for Understanding Bacterial and Archaeal Genomes.
  Imperial College Press, London, ISBN-13: 978-1-86094-982-1.
• Huang J, Gogarten JP (2008)
  Concerted gene recruitment in early plant evolution.
  Genome Biology 9(7): R109
• Fournier GP, Gogarten JP (2008)
  Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia.
  J. Bacteriol. 190(3):1124-7
• Huang, Jinling and J. Peter Gogarten (2007)
  Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?
  Genome Biology 8(6): R99
• Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F., and Papke, R.T. (2006)
  Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. 
  Genome Research 16(9):1099-108
• Gogarten, J.P. and Hilario, E. (2006)
  Inteins, introns, and homing endonucleases: Recent revelations about the life cycle of parasitic genetic elements. 
  BMC Evolutionary Biology 6:94
• Huang, J. and Gogarten, J.P. (2006) Ancient horizontal gene transfer can benefit phylogenetic reconstruction.
  Trends in Genetics 22(7):361-6.
• Lapierre P, Shial R, Gogarten JP (2006): Distribution of F- and A/V- type ATPases in Thermus scotoductus and Other Closely Related Species.
  Systematic and Applied Microbiology 29(1):15-23
• Zhaxybayeva, O., Lapierre, P., and Gogarten, J. P. (2006): Ancient Gene Duplications and the Root(s) of the Tree of Life.
  Protoplasma 227(1): 53-64
• Gogarten, J. P., and Townsend, J. P. (2005): Horizontal gene transfer, genome innovation, and evolution.
  Nature Reviews in Microbiology 3(9) 679-687
• Huang J., Xu, Y,. and Gogarten, J.P. (2005): The Presence of a Haloarchaeal Type Tyrosyl tRNA Synthetase Marks theOpisthokonts as Monophyletic. 
  Molecular Biology and Evolution 22(11): 2142-6
• Zhaxybayeva, O. and Gogarten, J.P. (2004):
  Cladogenesis, Coalescence and the Evolution of the Three Domains of Life.
  Trends in Genetics 20 (4): 182- 187
• Raymond, J., Zhaxybayeva, O., Gogarten,J.P., Gerdes, S., Blankenship, R.E. (2002):
  Whole Genome Analysis of Photosynthetic Prokaryotes.
  Science 298: 1616-1620.
• Gogarten, J. P., Doolittle, W. F. and Lawrence, J. G. (2002): Prokaryotic Evolution in Light of Gene Transfer.
  Molecular Biology and Evolution 19: 2226-2238.
• Gogarten, J. P., Senejani, A. G., Zhaxybayeva, O., Olendzenski, L. and Hilario, E. (2002)
  Inteins: Structure, Function, and Evolution. 
  Annu. Rev. Microbiol. 56: 263-287
• Zhaxybayeva O, Gogarten JP (2002) Bootstrap, Bayesian probability and maximum likelihood mapping: Exploring new tools for comparative genome analyses. 
  BMC Genomics3:4,1-13
• Olendzenski, L., Liu, L., Zhaxybayeva, O., Murphey, R., Shin, D.-G., and Gogarten, J.P. (2000):
  Horizontal Transfer of Archaeal Genes into the Deinococcaceae: Detection by molecular and computer based approaches.
  Journal of Molecular Evolution, 51(6): 587-599.
• Gogarten JP, Oldendzenski L, Hilario E, Simon C, Holsinger KE (1996)
  Dating the Cenancester of Organisms – Technical Comment,
  Science, 274, 1750-1751.
• Gogarten-Boekels M, Hilario E, Gogarten JP (1995)
  The effects of heavy meteorite bombardment on the early evolution – the emergence of the three domains of life.
  Origin of Life and Evolution of the Biosphere, 25, 251-264
• Hilario, E, Gogarten, J.P. (1993):
  Horizontal Transfer of ATPase Genes -The Tree of Life becomes a Net of Life, 
  BioSystems 31, 111-119.
• Gogarten, J.P., Kibak, H., Dittrich, P. Taiz, L., Bowman, E.J., Bowman, B., Manolson, M., Poole, R., Date, T., Oshima, T., Konishi, J., Denda, K., Yoshida, M. (1989)
  The evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes.
  Proceedings of the National Academy of Sciences U.S.A. 86, 6661-6665