The Incredible Shrinking Genome Utricularia gibba Enrique Ibarra-Laclette2, Eric Lyons1, Gustavo Hernandez3, Anahi Perez- Torres2, Lorenzo Carretero-Paulet4, Tien-Hao Chang4, Tianying Lan4, Andreanna Welch4, Maria Jazmin Abraham Juarez2, June Simpson2, Araceli Fernandez- Cortez2, Mario Arteaga-Vazquez5, Elsa Gongora-Castillo6, Gustavo Acevedo- Hernandez7, Stephan C. Schuster8, Heinz Himmelbauer9, Andre E. Minoche9, Sen Xu10, Michael Lynch10, Araceli Oropeza-Aburto2, Sergio Alan Cervantes-Perez2, Maria de Jesus Ortega-Estrada2, Jacob Israel Cervantes-Luevano2, Todd P. Michael11, Todd C. Mockler12, Doug Bryant12, Alfredo Herrera-Estrella2, Victor A. Albert4, Luis Herrera-Estrella2 1 University of Arizona 7 Centro Universitario de la Cienega 2 CINVESTAV 8 Pennsylvania State University 3 Universidad de Guanajuato 9 Center for Genomic Regulation, CRG 4 University at Buffalo 10 Indiana University 5 Instituto de Biotecnologia y Ecologia Aplicada 11 Rutgers University 6 Michigan State University 12 Donald Danforth Plant Science Center Who is Utricularia gibba? The humped blatterwort source: USDA source: The Royal Society U. gibba: genome stats ~82MB genome size CDS GC Content Should be an easy genome to characterize paleo-polyploidy Few or no active retrotransposons http://genomevolution.org/r/6bx0 Sequenced Plant Genomes http://genomevolution.org/r/3118 Thanks: James Schnable Utricularia gibba core eudicotyledons; asterids; lamiids; Lamiales; Lentibulariaceae; Utricularia MOBOT Characterizing paleo-polyploidy http://polyploidy.iplantc.org Utricularia gibba Eurosid Paleohexaploidy (WGT) Utricularia WGD Mimulus is closest, but under-characterized Tomato is well characterized, but has a WGT Grape is the de facto eurosid outgroup comparator Comparative Genomics Sequence Microsynteny similarity Sequence 1 Sequence 2 http://genomevolution.org/r/6jyz Syntenic dotplot Gene model Gene overlapped CoGe link to by sequence similarity regenerate the analysis Synteny: genomic regions sharing a common ancestry Synteny: inferred by a Duplication Colinear genes colinear arrangement of homologous genes Genome 2 Genome http://genomevolution.org/r/5yet Genome 1 Syntenic Path Assembly Making sense of NextGen Genome Assemblies Utricularia: NextGen Assembly with ~5000 contigs Syntenic Path Assembly Making sense of NextGen Genome Assemblies Escherichia coli K12 strain K-12 substrain MG1655 Escherichia coli K12 strain K-12 substrain E4370 Syntenic Path Assembly Using synteny to assemble to a reference genome Assembled by Syntenic Path Escherichia coli K12 strain K-12 substrain MG1655 Escherichia coli K12 strain K-12 substrain E4370 Self-self Utricularia ! CoGe SynMap: http://genomevolution.org/r/6lid Self-self Utricularia Assembled by Syntenic Path CoGe SynMap: http://genomevolution.org/r/6lib Evidence for 2xTetraploidy Utricularia Self-Self Sytnenic Dotplot: Synonymous Subsitutions (ks) Most recent WGD Log10 Ks values Second Most recent WGD Most recent WGD http://genomevolution.org/r/6g6j Evidence for 2xWDG Utricularia Microsynteny Analysis U1 U2 U3 U4 http://genomevolution.org/r/6g76 Evidence for 2xWDG Utricularia Microsynteny Analysis Signal of intragenomic synteny degrades over time through diploidization process: fractionation (deletion of homeologous genes) Exacerbated by additional polyploidy events U1 Most recent WGD U2 Second most recent WGD U3 Most recent WGD U4 http://genomevolution.org/r/6g76 Fractionation and diploidization: (Importance of outgroups) Ancestor Genome duplication R1 R1’ Gene Loss / Fractionation R1 Syntelogs R1’ R1 Unduplicated Outgroup R1’ Intercalated Colinear Genes Sequenced Plant Genomes http://polyploidy.iplantc.org Utricularia gibba Need to understand Mimulus’ genome evolution in order to compare to Utricularia Utricularia WGD Mimulus is closest, but under-characterized Tomato is well characterized, but has a WGT Grape is the de facto eurosid outgroup comparator Mimulus has a WGD Self-self Mimulus Mimulus v. Grape ! Grape (Vitis vinifera) Grape(Vitis Mimulus Grape http://genomevolution.org/r/6eqq http://genomevolution.org/r/6lzr Mimulus Mimulus has a WGD Self-self Mimulus Mimulus v. Grape Mg1 Vv Mg2 http://genomevolution.org/r/8sr6 ! Grape (Vitis vinifera) Grape(Vitis Mimulus Grape http://genomevolution.org/r/6eqq http://genomevolution.org/r/6lzr Mimulus Mimulus has a WGD Self-self Mimulus Mimulus v. Grape Mimulus had a WGD subsequent to the eurosid paleohexaploidy Mg1 2xMg:1xVv Vv Mg2 http://genomevolution.org/r/8sr6 ! Grape (Vitis vinifera) Grape(Vitis Mimulus Grape http://genomevolution.org/r/6eqq http://genomevolution.org/r/6lzr Intercalated Colinear Genes Mimulus Utricularia v. Mimulus 4xUg:1xMg? Utricularia Utricularia Mimulus http://genomevolution.org/r/6erk Mimulus ! 4:1 Utricularia to Mimulus Ug1 Ug2 Ug3 Ug4 Mg http://genomevolution.org/r/8srb Intercalated Colinear Genes 4:1 Utricularia to Mimulus (x2) ! Ug1 Ug1 Ug2 Ug1 Ug3 Ug1 Ug4 Ug1 Mg1 Mg1 Mg2 Mg2 Ug5 Ug1 Ug6 Ug1 Ug7 Ug1 Ug8 Ug1 http://genomevolution.org/r/6m07 http://genomevolution.org/r/6l1rhttp://genomevolution.org/r/6l1r WGD Ug1 WGD Ug2 Ug3 WGD Ug4 Mg1 1x Grape Vv 2x Mimulus 8x Utricularia Mg2 http://genomevolution.org/r/6lkd Ug5 Ug6 Ug7 Ug8 Conclusions Utricularia has had three sequential tetraploidy events (8x) subsequent to the Eudicot paleohexaploidy, despite having a small(est) plant genome Utricularia’s oldest WGD is likely shared with Mimulus; (independent of the Tomato WGT) Genome Size is a function of genome expansion and contraction mechanisms Conclusions Utricularia has had three sequential tetraploidy events (8x) subsequent to the Eudicot paleohexaploidy, despite having a small(est) plant genome Utricularia’s oldest WGD is likely shared with Mimulus; (independent of the Tomato WGT) Genome Size is a function of genome expansion and contraction mechanisms RBG Kew DNA C-values query results Thanks Download this presentation: http://genomevolution.org/r/8t6y Utricularia gibba sequencing and analysis team: Enrique Ibarra-Laclette, Gustavo Hernandez, Anahi Perez-Torres, Lorenzo Carretero-Paulet, Tien-Hao Chang, Tianying Lan, Andreanna Welch, Maria Jazmin Abraham Juarez, June Simpson, Araceli Fernandez-Cortez, Mario Arteaga- Vazquez, Elsa Gongora-Castillo, Gustavo Acevedo-Hernandez, Stephan C. Schuster, Heinz Himmelbauer, Andre E. Minoche, Sen Xu, Michael Lynch, Araceli Oropeza-Aburto, Sergio Alan Cervantes-Perez, Maria de Jesus Ortega-Estrada, Jacob Israel Cervantes-Luevano, Todd P. Michael, Todd C. Mockler, Doug Bryant, Alfredo Herrera-Estrella, Victor A. Albert, Luis Herrera-Estrella CoGe Team: Matt Bomhoff, Evan Briones, Haibao Tang Comparative Genomics Collaborators: Haibao Tang: SynMap; SynFind James Schnable: Plant polyploidy iPlant Collaborative: Many, many people!.