The Incredible Shrinking Genome Utricularia gibba Enrique - - PowerPoint PPT Presentation

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The Incredible Shrinking Genome Utricularia gibba Enrique - - PowerPoint PPT Presentation

May 04, 2023 114 likes •394 views

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

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SLIDE 1

The Incredible Shrinking Genome

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

Utricularia gibba

1 University of Arizona 2 CINVESTAV 3 Universidad de Guanajuato 4 University at Buffalo 5 Instituto de Biotecnologia y Ecologia Aplicada 6 Michigan State University 7 Centro Universitario de la Cienega 8 Pennsylvania State University 9 Center for Genomic Regulation, CRG 10 Indiana University 11 Rutgers University 12 Donald Danforth Plant Science Center

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SLIDE 2

Who is Utricularia gibba?

The humped blatterwort

source: USDA

source: The Royal Society

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SLIDE 3
  • U. gibba: genome stats

~82MB genome size

CDS GC Content

Few or no active retrotransposons

http://genomevolution.org/r/6bx0

Should be an easy genome to characterize paleo-polyploidy

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SLIDE 4

Sequenced Plant Genomes

Thanks: James Schnable

Utricularia gibba

MOBOT

core eudicotyledons; asterids; lamiids; Lamiales; Lentibulariaceae; Utricularia http://genomevolution.org/r/3118

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SLIDE 5

Utricularia gibba

Utricularia WGD

Mimulus is closest, but under-characterized Grape is the de facto eurosid outgroup comparator Tomato is well characterized, but has a WGT

http://polyploidy.iplantc.org Eurosid Paleohexaploidy (WGT)

Characterizing paleo-polyploidy

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SLIDE 6

Comparative Genomics

http://genomevolution.org/r/6jyz

Microsynteny

Gene model Sequence similarity Gene overlapped by sequence similarity Sequence 1 Sequence 2 CoGe link to regenerate the analysis

Syntenic dotplot

Genome 2 Genome 1 Colinear genes

Synteny: genomic regions sharing a common ancestry Synteny: inferred by a colinear arrangement of homologous genes

http://genomevolution.org/r/5yet Duplication

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SLIDE 7

Utricularia: NextGen Assembly with ~5000 contigs

Syntenic Path Assembly

Making sense of NextGen Genome Assemblies

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SLIDE 8

Escherichia coli K12 strain K-12 substrain E4370

E s c h e r i c h i a c

  • l

i K 1 2 s t r a i n K

  • 1

2 s u b s t r a i n M G 1 6 5 5

Syntenic Path Assembly

Making sense of NextGen Genome Assemblies

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SLIDE 9

Using synteny to assemble to a reference genome

Escherichia coli K12 strain K-12 substrain E4370

E s c h e r i c h i a c

  • l

i K 1 2 s t r a i n K

  • 1

2 s u b s t r a i n M G 1 6 5 5

Assembled by Syntenic Path

Syntenic Path Assembly

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SLIDE 10

Self-self Utricularia

!

CoGe SynMap: http://genomevolution.org/r/6lid

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SLIDE 11

Self-self Utricularia

CoGe SynMap: http://genomevolution.org/r/6lib

Assembled by Syntenic Path

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SLIDE 12

Evidence for 2xTetraploidy

http://genomevolution.org/r/6g6j

Utricularia Self-Self Sytnenic Dotplot: Synonymous Subsitutions (ks)

Most recent WGD

Second Most recent WGD

Log10 Ks values

Most recent WGD

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SLIDE 13

http://genomevolution.org/r/6g76

Evidence for 2xWDG

Utricularia Microsynteny Analysis

U1 U2 U3 U4

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SLIDE 14

http://genomevolution.org/r/6g76

Evidence for 2xWDG

Utricularia Microsynteny Analysis

U1 U2 U3 U4

Signal of intragenomic synteny degrades

  • ver time through diploidization process:

fractionation (deletion of homeologous genes) Exacerbated by additional polyploidy events Most recent WGD Most recent WGD Second most recent WGD

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SLIDE 15

Fractionation and diploidization:

Ancestor

Gene Loss / Fractionation

R1 R1’ R1 R1’

Genome duplication

Syntelogs

R1 R1’

Unduplicated Outgroup Intercalated Colinear Genes (Importance of outgroups)

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SLIDE 16

Sequenced Plant Genomes

Utricularia gibba

Utricularia WGD

Mimulus is closest, but under-characterized Grape is the de facto eurosid outgroup comparator Tomato is well characterized, but has a WGT

http://polyploidy.iplantc.org

Need to understand Mimulus’ genome evolution in order to compare to Utricularia

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SLIDE 17

Grape (Vitis vinifera)

Self-self Mimulus

http://genomevolution.org/r/6lzr http://genomevolution.org/r/6eqq

Mimulus v. Grape

!

Mimulus has a WGD

Mimulus Grape Mimulus

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SLIDE 18

Grape (Vitis vinifera)

Self-self Mimulus

http://genomevolution.org/r/6lzr http://genomevolution.org/r/6eqq

Mimulus v. Grape

!

Mimulus has a WGD

Vv Mg1 Mg2

http://genomevolution.org/r/8sr6

Mimulus Grape Mimulus

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SLIDE 19

Grape (Vitis vinifera)

Self-self Mimulus

http://genomevolution.org/r/6lzr http://genomevolution.org/r/6eqq

Mimulus v. Grape

!

Mimulus has a WGD

Vv Mg1 Mg2

http://genomevolution.org/r/8sr6

Intercalated Colinear Genes

Mimulus had a WGD subsequent to the eurosid paleohexaploidy

Mimulus

2xMg:1xVv

Grape Mimulus

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SLIDE 20

Utricularia v. Mimulus

http://genomevolution.org/r/6erk

!

4xUg:1xMg?

Utricularia Mimulus Utricularia Mimulus

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SLIDE 21

4:1 Utricularia to Mimulus

http://genomevolution.org/r/8srb

Ug1 Ug2 Ug3 Ug4 Mg

Intercalated Colinear Genes

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SLIDE 22

! http://genomevolution.org/r/6l1r Ug1 Ug1 Ug1 Ug1 Ug1 Ug1 Ug1 Ug1 Mg1 Mg2

4:1 Utricularia to Mimulus (x2)

http://genomevolution.org/r/6m07 http://genomevolution.org/r/6l1r

Ug1 Ug2 Ug3 Ug4 Mg1 Mg2 Ug5 Ug6 Ug7 Ug8

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SLIDE 23

http://genomevolution.org/r/6lkd

Vv Mg1 Mg2 Ug1 Ug2 Ug3 Ug4 Ug5 Ug6 Ug7 Ug8

1x Grape 2x Mimulus 8x Utricularia

WGD WGD WGD

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SLIDE 24

Conclusions

Utricularia has had three sequential tetraploidy events (8x) subsequent to the Eudicot paleohexaploidy, despite having a small(est) plant genome

Genome Size is a function of genome expansion and contraction mechanisms

Utricularia’s oldest WGD is likely shared with Mimulus; (independent of the Tomato WGT)

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SLIDE 25

Conclusions

Utricularia has had three sequential tetraploidy events (8x) subsequent to the Eudicot paleohexaploidy, despite having a small(est) plant genome

Genome Size is a function of genome expansion and contraction mechanisms

Utricularia’s oldest WGD is likely shared with Mimulus; (independent of the Tomato WGT)

RBG Kew DNA C-values query results

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SLIDE 26

Thanks

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!

Download this presentation: http://genomevolution.org/r/8t6y