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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