The Incredible Shrinking Genome Utricularia gibba Enrique - PowerPoint PPT Presentation

The Incredible Shrinking Genome Utricularia gibba Enrique Ibarra-Laclette 2 , Eric Lyons 1 , Gustavo Hernandez 3 , Anahi Perez- Torres 2 , Lorenzo Carretero-Paulet 4 , Tien-Hao Chang 4 , Tianying Lan 4 , Andreanna Welch 4 , Maria Jazmin Abraham Juarez 2 , June Simpson 2 , Araceli Fernandez- Cortez 2 , Mario Arteaga-Vazquez 5 , Elsa Gongora-Castillo 6 , Gustavo Acevedo- Hernandez 7 , Stephan C. Schuster 8 , Heinz Himmelbauer 9 , Andre E. Minoche 9 , Sen Xu 10 , Michael Lynch 10 , Araceli Oropeza-Aburto 2 , Sergio Alan Cervantes-Perez 2 , Maria de Jesus Ortega-Estrada 2 , Jacob Israel Cervantes-Luevano 2 , Todd P . Michael 11 , Todd C. Mockler 12 , Doug Bryant 12 , Alfredo Herrera-Estrella 2 , Victor A. Albert 4 , Luis Herrera-Estrella 2 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 Bu ff alo 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 Syntenic dotplot http://genomevolution.org/r/6jyz Gene overlapped Gene model by sequence similarity CoGe link to regenerate the analysis Synteny: genomic regions sharing a common ancestry Synteny: inferred by a Duplication Colinear genes Genome 2 colinear arrangement of homologous genes 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 5 5 6 1 G M n i a r t s b u s 2 1 - K n i a r t s 2 1 K i l o c a i h c i r e h c s E Escherichia coli K12 strain K-12 substrain E4370

Syntenic Path Assembly Using synteny to assemble to a reference genome Assembled by Syntenic Path 5 5 6 1 G M n i a r t s b u s 2 1 - K n i a r t s 2 1 K i l o c a i h c i r e h c s E 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 Mimulus http://genomevolution.org/r/6eqq http://genomevolution.org/r/6lzr Mimulus

Mimulus has a WGD Self-self Mimulus Mimulus v. Grape Mg1 Grape (Vitis vinifera) Vv Mg2 http://genomevolution.org/r/8sr6 ! Grape Mimulus 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 Grape (Vitis vinifera) 2xMg:1xVv Vv Mg2 http://genomevolution.org/r/8sr6 ! Grape Mimulus 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 Ug1 Ug2 Ug3 Ug1 Ug4 Ug1 Mg1 Mg1 Mg2 Mg2 Ug5 Ug1 Ug1 Ug6 Ug1 Ug7 Ug1 Ug8 http://genomevolution.org/r/6m07 http://genomevolution.org/r/6l1r http://genomevolution.org/r/6l1r

WGD Ug1 WGD Ug2 Ug3 WGD Ug4 http://genomevolution.org/r/6lkd 1x Grape Mg1 2x Mimulus Vv 8x Utricularia Mg2 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!