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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 Arizona2 CINVESTAV3 Universidad de Guanajuato 4 University at Buffalo5 Instituto de Biotecnologia y Ecologia Aplicada6 Michigan State University

7 Centro Universitario de la Cienega8 Pennsylvania State University9 Center for Genomic Regulation, CRG10 Indiana University11 Rutgers University12 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

Few or no active retrotransposons

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

Should be an easy genome to characterize paleo-polyploidy

Sequenced Plant GenomesThanks: James Schnable

Utr

icul

aria

gib

ba

MOBOT

core eudicotyledons; asterids; lamiids; Lamiales; Lentibulariaceae; Utricularia

http://genomevolution.org/r/3118

Utr

icul

aria

gib

ba

Utricularia WGDMimulus 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

Comparative Genomics

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

Microsynteny

Gene model

Sequencesimilarity

Gene overlapped by sequence similarity

Sequence 1

Sequence 2

CoGe link to regenerate the analysis

Syntenic dotplot

Gen

ome

2

Genome 1

Colinear genes

Synteny: genomic regions sharing a common ancestry

Synteny: inferred by a colinear arrangement of

homologous geneshttp://genomevolution.org/r/5yet

Duplication

Utricularia: NextGen Assemblywith ~5000 contigs

Syntenic Path AssemblyMaking sense of NextGen Genome Assemblies

Escherichia coli K12 strain K-12 substrain E4370

Esch

erich

ia c

oli K

12 s

train

K-1

2 su

bstra

in M

G16

55

Syntenic Path AssemblyMaking sense of NextGen Genome Assemblies

Using synteny to assemble to a reference genome

Escherichia coli K12 strain K-12 substrain E4370

Esch

erich

ia c

oli K

12 s

train

K-1

2 su

bstra

in M

G16

55

Assembled by Syntenic Path

Syntenic Path Assembly

Self-self Utricularia!

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

Self-self Utricularia

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

Assembled by Syntenic Path

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 recentWGD

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

Evidence for 2xWDGUtricularia Microsynteny Analysis

U1

U2

U3

U4

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

Evidence for 2xWDGUtricularia Microsynteny Analysis

U1

U2

U3

U4

Signal of intragenomic synteny degrades over time through diploidization process:

fractionation (deletion of homeologous genes)

Exacerbated by additional polyploidy events

Most recent WGD

Most recent WGD

Second most recent WGD

Fractionation and diploidization:Ancestor

Gene Loss / Fractionation

R1

R1’

R1

R1’

Genome duplication

Syntelogs

R1

R1’

UnduplicatedOutgroup

Intercalated Colinear Genes

(Importance of outgroups)

Sequenced Plant GenomesU

tric

ular

ia g

ibba

Utricularia WGDMimulus 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

Gra

pe (V

itis v

inife

ra)

Self-self Mimulus

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

Mimulus v. Grape

!

Mimulus has a WGD

Mimulus Gra

pe

Mimulus

Gra

pe (V

itis v

inife

ra)

Self-self Mimulus

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

Mimulus v. Grape

!

Mimulus has a WGD

Vv

Mg1

Mg2http://genomevolution.org/r/8sr6

Mimulus Gra

pe

Mimulus

Gra

pe (V

itis v

inife

ra)

Self-self Mimulus

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

Mimulus v. Grape

!

Mimulus has a WGD

Vv

Mg1

Mg2http://genomevolution.org/r/8sr6

Intercalated Colinear Genes

Mimulus had a WGD subsequent to the eurosid paleohexaploidy

Mimulus

2xMg:1xVv

Gra

pe

Mimulus

Utricularia v. Mimulus

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

!

4xUg:1xMg?

Utric

ular

ia

Mimulus

Utric

ular

ia

Mimulus

4:1 Utricularia to Mimulus

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

Ug1

Ug2

Ug3

Ug4

Mg

Intercalated Colinear Genes

!

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

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

Vv

Mg1

Mg2

Ug1

Ug2

Ug3

Ug4

Ug5

Ug6

Ug7

Ug8

1x Grape2x Mimulus

8x Utricularia

WGD

WGDWGD

ConclusionsUtricularia 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)

ConclusionsUtricularia 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

ThanksUtricularia 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