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.