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![Page 1: The Incredible Shrinking Genome › ~mabrouk › MAGE2013 › slides › Eric-Lyons...The Incredible Shrinking Genome Enrique Ibarra-Laclette2, Eric Lyons1, Gustavo Hernandez3, Anahi](https://reader034.vdocuments.net/reader034/viewer/2022050719/5f22dcba8074ed2b67235430/html5/thumbnails/1.jpg)
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
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Who is Utricularia gibba?The humped blatterwort
source: USDA
source:The Royal
Society
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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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Sequenced Plant GenomesThanks: James Schnable
Utr
icul
aria
gib
ba
MOBOT
core eudicotyledons; asterids; lamiids; Lamiales; Lentibulariaceae; Utricularia
http://genomevolution.org/r/3118
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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
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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
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Utricularia: NextGen Assemblywith ~5000 contigs
Syntenic Path AssemblyMaking sense of NextGen Genome Assemblies
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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
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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
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Self-self Utricularia!
CoGe SynMap: http://genomevolution.org/r/6lid
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Self-self Utricularia
CoGe SynMap: http://genomevolution.org/r/6lib
Assembled by Syntenic Path
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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
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http://genomevolution.org/r/6g76
Evidence for 2xWDGUtricularia Microsynteny Analysis
U1
U2
U3
U4
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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
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Fractionation and diploidization:Ancestor
Gene Loss / Fractionation
R1
R1’
R1
R1’
Genome duplication
Syntelogs
R1
R1’
UnduplicatedOutgroup
Intercalated Colinear Genes
(Importance of outgroups)
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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
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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
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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
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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
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Utricularia v. Mimulus
http://genomevolution.org/r/6erk
!
4xUg:1xMg?
Utric
ular
ia
Mimulus
Utric
ular
ia
Mimulus
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4:1 Utricularia to Mimulus
http://genomevolution.org/r/8srb
Ug1
Ug2
Ug3
Ug4
Mg
Intercalated Colinear Genes
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!
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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http://genomevolution.org/r/6lkd
Vv
Mg1
Mg2
Ug1
Ug2
Ug3
Ug4
Ug5
Ug6
Ug7
Ug8
1x Grape2x Mimulus
8x Utricularia
WGD
WGDWGD
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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)
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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
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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