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Jean-Francois Pombert

Jean-Francois Pombert, Ph.D.

Jean-Francois Pombert
Assistant Professor of Biology






LS 296


Ph.D. in Biochemistry, Universite Laval 2008

Research & Accomplishments 

My research revolves mostly around comparative genomics, with an emphasis on finding the elements that distinguish obligate pathogens from their free-living relatives. I am particularly interested by key protists that could help us better understand the evolution of pathogenicity and by microbiomes and their associated diseases. I am also interested by unknown or poorly understood organisms and work with species widely dispersed across the Tree of Life.


  • Comparative genomics, Computational biology/bioinformatics, High-throughput DNA sequencing


  • Oral microbiome, Green algal genomics, Pathogen genomics


2013 Pombert JF, Smirnov A, James ER, Janouškovec J, Gray MW and Keeling PJ. The complete mitochondrial genome from an unidentified Phalansterium species. Submitted to Protist Genomics.

2013 Pombert JF, Xu J, Smith DR, Heiman D, Young S, Cuomo CA, Weiss LM and Keeling PJ. Complete genome sequences from three genetically distinct strains reveal a high intra-species genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryotic Cell. 12(4): 503-511.

2012 Pombert JF, Selman M, Burki F, Bardell FT, Farinelli L, Solter LF, Whitman DW, Weiss LM, Corradi N and Keeling PJ. The gain and loss of multiple functionally-related horizontally transferred genes to the miniaturised genomes of two microsporidian parasites. PNAS 109(31): 12638-12643.

2012 Pombert JF, James ER, Janouškovec J and Keeling PJ. Evidence for transitional stages in the evolution of euglenid group II and group III introns and twintrons in the Monomorphina aenigmatica plastid genome. PLoS ONE 5(1): e8954.

2012 Pelin A, Pombert JF, Salvioli A, Bonen L, Bonfante P and Corradi N. The mitochondrial genome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals two unsuspected trans-splicing events of group I introns. New Phytologist. 194:836-845.

2012 Imanian B, Pombert JF, Dorrell RG and Keeling PJ. Tertiary endosymbiosis in two dinotoms has generated little change in the mitochondrial genomes of their dinoflagellate hosts and diatom endosymbionts. PLoS ONE 7(8): e43763.

2012 Oleksyk TK, Pombert JF, Siu D, Mazo-Vargas A, Ramos B, Guiblet W, Afanador Y, Ruiz-Rodriguez CT, Nickerson ML, Dean M, Logue D, Figueroa L, Valentin R, Rodriguez-Flores JL, Massey SE, Martinez-Cruzado JC. A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education. GigaScience. 1:14.

2012 Burki F, Okamoto N, Pombert JF and Keeling PJ. Phylogenomic evidence for the separate origins of haptophytes and cryptophytes. Proc. R. Soc. B. 279: 2246-2254.

2011 Selman M, Pombert JF, Solter L, Farinelli L, Weiss LM, Keeling PJ and Corradi N. Acquisition of an animal gene by microsporidian intracellular parasites. Current Biology 21(15): R1-R2.

2011 Oleksyk TK, Pombert JF, Guiblet W, Ramos B, Mazo A, Ruiz-Rodriguez CT, Nickerson ML, Winkler CA, Siu D, Valentin R, Figueroa L, Dean M, Logue D and Martinez-Cruzado JC. A Draft sequence of the Puerto Rican parrot genome (Amazona vittata) - a genome project funded by a local community effort. Nature Precedings npre.2011.6552.1. (Not peer-reviewed).

2011 Gosh K, Nieves E, Keeling PJ, Pombert JF, Henrich PP, Cali A and Weiss LM. A branching network of proteinaceous filaments within the parasitophorous vacuole of Encephalitozoon cuniculi and Encephalitozoon hellem. Infection and Immunity 79(3):1374-1385.

2010 Pombert JF and Keeling PJ. The mitochondrial genome of the entomoparasitic green alga Helicosporidium. PLoS ONE 5(1): e8954.

2010 Corradi C, Pombert JF, Farinelli L, Didier ES and Keeling PJ. The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nature Communications. 1:77.

2010 Imanian B, Pombert JF and Keeling PJ. The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum. PLoS ONE. 5(5): e10711.

2009 Pombert JF, Sistek V, Boissinot M and Frenette M. Evolutionary relationships among salivarius streptococci as inferred from multilocus phylogenies based on 16S rRNA-encoding, recA, secA, and secY gene sequences. BMC Microbiology 9:232.

2009 Corradi C, Haag KL, Pombert JF, Ebert D and Keeling PJ. Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. Genome Biology 10:R106.

2007 Turmel M, Pombert JF, Charlebois P, Otis C and Lemieux C. The green algal ancestry of land plants as revealed by the chloroplast genome. International Journal of Plant Sciences 168:679–689.

2006 Pombert JF, Beauchamp P, Otis C, Lemieux C and Turmel M. The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: Evolutionary trends of the mitochondrial genome in the Ulvophyceae. Current Genetics 50:137-147.

2006 Pombert JF, Lemieux C and Turmel M. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes. BMC Biology 4:3.

2005 Pombert JF, Otis C, Lemieux C and Turmel M. The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Molecular Biology and Evolution 22:1903-1918.

2004 Pombert JF, Otis C, Lemieux C and Turmel M. The complete mitochondrial DNA sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) highlights distinctive evolutionary trends in the Chlorophyta and suggests a sister-group relationship between the Ulvophyceae and Chlorophyceae. Molecular Biology and Evolution 21:922-935.