Evolution of Animal Body Plans
Holland 2003 Nature Reviews Neuroscience Vol 4.
Ctenophores?
Modified from
Pang et al 2010
Combination of markersEST Sequences
Phylogenomic Data
Morphological Data 18S rDNA
Phylogenomic Data + More ESTs
The position of Ctenophora on the
Metazoan tree is unresolved
Placozoa – creeping detritivore/algavore, diploblastic, continually change shape
Cnidaria – planktonic or sessile predators, diploblastic, radial symmetry
Basal Metazoans exhibit a wide variety of body plans and life history strategies
Porifera (Sponges) – sessile filter feeders, no true tissues, asymmetry
Ctenophora (Comb Jellies) – active predators in the plankton, triploblastic, bi-radial symmetry
Joint Genome Institute
Andrea Kohn Leonid Moroz
Billie SwallaMat Citrella
2010 and 2012
Genomics
Apprenticeships
At FHL
The Early Evolution of Nervous System Development:
Genomics of Pleurobrachiabachia
Undergraduate Research Apprenticeship
Genome Biology
• Undergraduate students engaged in field activities• Enhance computational skills• Clone genes and examine gene expression to study evolution of nerve networks with marine invertebrates as a collaborative research experience.
• Instructors and/or themes vary from year to year• FHL has housing, dining facilities & a computer classroom• Students are recruited from UW and other universities
Friday Harbor Labs - San Juan Island
Beautiful setting, amazing biological diversity, all students doing research in the course, few distractions for them.
New Computer Lab for teaching Computational MethodsBioinformatics/Modelling/Phylogenetics/Genomics
Specific genes inform us about animalsCell-Cell adhesion (Collagens) NathanGerm Line
(Piwi) - Caleb(Nanos)-Gabby
Epigenomics (DNMT) - EmilyCell-Cell signaling (WNTs) - RebeccaMesoderm ?
(Brachyury, BarX) - Isaac(Tropomyosin, Calponin, ß catenin) -
ZanderNeuronal Development (LIMs) - RachelNeuronal Signaling (Glutamatergicpathway) - JoshNeuropeptides - David
Evolution of Animal Body PlansInsights from Marine Genomics
FHL Apprenticeship 2012
Ctenophores are small marine organisms
Ctenophores are basal metazoans
Figure 1. Basal metazoan phylogenetic relationship. From Dunn et al. 2008.
Placozoa
Cnidaria
Porifera
Ctenophora
Choanozoa(non-animal)
Bilateria
Ctenophore anatomy Mouth
Stomach
Tentacle bulb
Combs
Apical organ
Tentacle
Figure 2. Pleurobrachiabacheianatomy.
The Apical Organ - one of the first centralized nervous
systems
Comb RowsBalancersStatolith
Dome
Polar Fields(PF)
The PleurobrachiabacheiGenome
• First ever genome from an FHL animal to be sequenced.– Being the first ctenophore
genome is both exciting and challenging because without the genomes of related organisms assembly must be done de novo.
– Having the genome allows for comparison of homologies between phyla –other attempts to place them are “speculative”.
• Size of genome = ~100-160 megabases
Photo Credit: Mat Citarella
The Pleurobrachia Genome
• Five separate libraries (3 fragmented, 2 paired-end) were constructed, but satisfactory annotation and assembly of the genome has not yet been accomplished.
–This is due to short fragments from sequencing technology and highly repetitive regions of the genome that cause problems in assembly.
• Currently:–Sequences: 5,431,390 reads–Bases: 1,924,202,519 bases–Coverage: 10X–Number of Contigs: 211,869–Average Contig Size: 1,086 base pairs–Scaffold
Genomic organization
of P2X
Kohn, AB. (2010) Phylogenomics of P2X receptors. Unpublished
1
Importance of The Wnt Signaling Pathway
• gastrulation
• germ layer specification
• axial polarity
• Patterning of limbs
• Central Nervous System Development
• Wntpathway is oncogenic when mutated
• Evolved in the metazoan common ancestor
Cell Membrane
LRP
Frizzled
Dishevelled
Β-cateninNucleus Axin
APC
Gsk-3
Β-catenin
Cytoplasm
p
Degraded
Secreted Frizzled
Antagonists
DickkopfWIFCeberus
Conservation of Wnt Pathway in
Pleurobrachia(OFF)
? ?
DNA
Pleurobrachia Wnt genes contain conserved Wnt domain characteristics
Pb Wnt X
WNTMl Wnt X
100aa
Domain organization:SMART database
WNTAq Wnt 2
WNT
=Exon
In Situ Probe
=Signal peptide
Wnt conservation between ctenophores
M. leidyi
P. bachei
Wnt Frizzled Dickkopf WIF Ceberus
Homo 19 Yes Yes Yes Yes
Saccoglossus
Branchiostoma 10+? Yes Yes No No
Drosophila 7 Yes No Yes No
Caenorhabditis 5 4 No No No
Capitella 12 Yes No? Yes No?
Lottiagigantea 11 Yes No? Yes No?
Nematostella 11 Yes Yes Yes No
Trichoplax 3 Yes No No No
Amphimedon3 Yes No No No
Pleurobrachia 3 Yes No No No
Mnemiopsis 4 Yes No No No
Monosiga 0 No No No NoChoanoflagellates
Ctenophores
Sponges
Placozoans
Cnidarians
Deuterostomes
Evolution of Wnt in the Animal Kingdom
Bilaterians
Ecdysozoa
Lophotrochozoa
Common Wnt Pathway Components present and missing in basal metazoans
Gene P. bachei M. leidyi A. queenslandica
Wnt 3 4 3
Frizzled (Fzd) 2 2 2
Secreted-frizzled
related protein
(Srfp)
Present Present Present
LRP Present Present Present
APC No? Partial Present Missing domains
Axin Dix-domain like
protein
Dix-domain like
protein
Axin domain with
no B-Catenin
binding domain
GSK3 Present Present Present
Dishevelled Present Present Present
B-catenin Present Present Present
TCF/LEF Present Present Present
CK1 Present Present Present
groucho Present Present Present
WIF Absent Absent Absent
Dickkopf Absent Absent Absent
Cerberus Absent Absent Absent
CREB-biding
Protein (CBP)
Present Present Present
Scientific Conclusions
• Pleurobrachiacan show us the minimum members ofsignaling pathways needed for function
• Wnt, TGFßand other developmental signals areexpressed in adult Pleurobrachia
• There may beinvolved as neurotransmitters in Pleurobrachia
Education Conclusions
• Students learn computational skills easily when they are immersed in a research experience
• Students become more engaged when they have their own specific project
• Speaking and writing skills are best taught over a period of time, with repetition.
• Some students work better in a team, others individually, but computational analyses allow flexibility in projects.
Acknowledgements
• Wonderful Professors: Dr. Andrea Kohn,Dr. LenoidMoroz, Dr. Billie
Swalla• Amazing TAs: Gabrielle Winters, Caleb
Bostwick, Emily Dabe, and Kevin Kocot.• The Best Bioinformaticians: Mat Citarella
and David Girardo.• Funding: FHL, NIH, and NSF.