3. 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
4. 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
5. Andrea Kohn Leonid Moroz
Billie Swalla
Mat Citrella
2010 and 2012
Genomics
Apprenticeships
At FHL
6. The Early Evolution of Nervous System
Development:
Genomics of Pleurobrachiabachia
7. 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
8. Friday Harbor Labs - San Juan Island
Beautiful setting, amazing biological diversity, all students doing research in the course, few
distractions for them.
9. New Computer Lab for teaching Computational Methods
Bioinformatics/Modelling/Phylogenetics/Genomics
10. Specific genes inform us about animals
Cell-Cell adhesion (Collagens) Nathan
Germ Line
(Piwi) - Caleb
(Nanos)-Gabby
Epigenomics (DNMT) - Emily
Cell-Cell signaling (WNTs) - Rebecca
Mesoderm ?
(Brachyury, BarX) - Isaac
(Tropomyosin, Calponin, ß catenin) -
Zander
Neuronal Development (LIMs) - Rachel
Neuronal Signaling (Glutamatergic
pathway) - Josh
Neuropeptides - David
Evolution of Animal Body Plans
Insights from Marine Genomics
FHL Apprenticeship 2012
14. The Apical Organ - one of the
first centralized nervous
systems
Comb Rows
BalancersStatolith
Dome
Polar Fields(PF)
15. 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
16. 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
18. 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
22. 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
Amphimedon
3 Yes No No No
Pleurobrachia 3 Yes No No No
Mnemiopsis 4 Yes No No No
Monosiga 0 No No No No
Choanoflagellates
Ctenophores
Sponges
Placozoans
Cnidarians
Deuterostomes
Evolution of Wnt in the Animal Kingdom
Bilaterians
Ecdysozoa
Lophotrochozoa
23. 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
24. 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
25. 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.
26. 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.
Hinweis der Redaktion
Ctenophores- also called comb jellies (Greek- ctene= comb, phore= carry)A phylum of small jelly-filled animals that live all throughout the world in marine habitats.Size- Pleurobrachiabachei – pea sized to large grapeMain feature are their combs or ctenes which are rows of cilia used for swimming. Predators which eat small marine animals.
Ctenophores are one of the most basally branched organisms. Relationship between all the basal metazoans has been an issue of debate. Placozoa- one species in this phyla “trichoplaxadhaerens”Cnidarians – jelliesPorifera – SpongesOur ctenophoresChoanozoa – choanoflagellates - outgroup- single celled organisms that aren’t considered animals, but are the closest relative of animals. Highly debated whether porifera or ctenophora branched off first.This tree supported from ***
Ctenophore anatomy-Highly coordinated ciliary movement and predation skills suggests complex nervous systemApical organ- nervous system structure
Apical organ- early brain?Their basal position in the Metazoa, along with the presence of a nervous system containing a nerve net and an apical organ make ctenophores the ideal candidate for studies concerning the early evolution of the nervous system
WHAT IS A SIGNALING PATHWAY EXPLAIN-Signaling pathway transduces a signal from the outside of the cell to the inside of the cell and interacts in a cascade of events to induce a specific response WHY ARE PLEUROBRACHIA a good system to look at this in??-Because they are a basal metazoan so we can gain key insight onto the early evolution of this pathway.
Things missing in PB-FOUND by doing genome wide search why having a sequenced genome is so nice
EXPLAIN THAT THIS IS ONE OF 3 WNT Genes found in PBWnt domain contains common charactorists of a secretory peptideContains signal peptide N- glycosylation sites22 conserved cysteines used for disulfide bonds
EXPLAIN THAT PB is missing a homolog to WNT A
Explain expansion occurs in common ancestor to cnidarians and bilitarians