Simple Animals, Complex Genomes Comparative genomics of sponges, sea anemones, and multicellular pancakes Mansi Srivastava Rokhsar Lab, Department of Molecular and Cell Biology, UC Berkeley Reddien Lab, Whitehead Institute for Biomedical Research
Feb 23, 2016
Simple Animals, Complex Genomes
Comparative genomics of sponges, sea anemones, and multicellular pancakes
Mansi SrivastavaRokhsar Lab, Department of Molecular and Cell Biology, UC Berkeley
Reddien Lab, Whitehead Institute for Biomedical Research
02.23.13
Outline
1. Introduction
2. Insights from genomic analyses
3. Linking genomic complexity to biological complexity
CNIDARIANSPLACOZOANS SPONGES
What is the genomic basis for the difference in complexity?
BILATERIANS
?
bilateral symmetry, centralized nervous systemtrue muscle
true gutnervous systemtissue grade
multicellularity
Three species were selected for genome sequencing
SEA ANEMONE SPONGEPLACOZOAN
Nematostella vectensis is a sea anemone
(Finnerty et al. 2004)Nematostella is a great lab rat
Trichoplax is a placozoan
(photo credits: Ana Signorovitch, Michael Eitel, Bernd Schierwater)
Amphimedon queenslandica is a spongeAdult
Larvae
(photo credits: Bernie Degnan)
ATTTGCATGCGTAATTCAAT
CGTAATTCAATGTGTGATTC
ATTTGCATGCGTAATTCAAT
CGTAATTCAATGTGTGATTC
ATTTGCATGCGTAATTCAATGTGTGATTC
These animal genomes have been sequenced using a Whole Genome Shotgun strategy
Nematostella(cnidarian)
Trichoplax(placozoan)
Amphimedon(sponge) Human C. elegans
(nematode)Drosophila(fruit fly)
Genome size (Mb) 450 98 190 3,000 97 120
Gene Models ~18,000 ~11,500 ~24,000 ~20,000 ~20,000 ~14,000
Genome
Genes
Proteins
These animal genomes have different sizes, but the numbers of genes/proteins are in the
same ballpark
exon intron
Before comparing their genomes, we need to know how these animals are related to each other
and to us
BILATERIANS BILATERIANS
* * * *
Not an ancient animal gene
Ancient animal gene Lost in sponges
* *
Orthologous protein sequences can reveal how organisms are related to each other
mouse humanfishfly
Live birth, hair, warm blood, four chambered heart
vertebrae
MTLPDCMW RKLPDCMWPIDWDCMWRLKMTPIR
MTLPDCMW RKLPDCMWPIDWDCMWRLKMTPIR
Placozoans represent a sister lineage to cnidarians and bilaterians
Bilateria
Cnidaria
Animals
CNIDARIANSPLACOZOANSSPONGES
Whole-genome data can resolve early animal relationships BILATERIANS
multicellularity
bilateral symmetry, centralized nervous systemtrue muscle
true gutnervous systemtissue grade
Previously, some developmental processes were thought to be conserved in the bilaterian
ancestor
A-P patterningHox complex
Gene structure or genome organization (except for the Hox cluster) were not known to be ancient
How do the structures of genes compare between animal genomes?
Genome
Genes
Proteins
exon intron
Sea anemones, placozoans, and sponges have preserved
many (>80%) ancient introns
(in collaboration with Uffe Hellsten)
(this is not the case for flies and nematodes, which have lost a majority of ancestral metazoan introns)
What about how genes are organized relative to each other?
The positions of orthologous genes can be compared between two species
Gene order conservation decreases with evolutionary distance
Synteny “same thread”genes present on the same chromosome
No chromosome scale synteny is observed between vertebrates and flies
Drosophila
Hum
an
Nematostella, Trichoplax, and Amphimedon scaffolds show conserved synteny with human chromosome
segments
(Nik Putnam)
There is considerable scrambling of gene order in these blocks of conserved synteny
(Nik Putnam)
What is the significance of this conserved synteny?
Another way to compare genomes is in terms of gene content…
Trichoplax has genes for neurons and epithelial cells
Trichoplax has genes for developmental signaling pathways
Early animal lineages may lack certain cell types or biological processes, but their genomes encode the
proteins required for these in bilaterians
Many “important” genes are involved in processes essential for animal multicellularity
Six hallmarks of animal multicellularity:
1. Regulated cell cycle and growth2. Programmed cell death3. Cell-cell and cell-matrix adhesion4. Allorecognition and innate
immunity5. Specialization of cell types6. Developmental signaling
Comparing early animal genomes allows us to study the temporal origins of animal biology
Six hallmarks of animal multicellularity:
1. Regulated cell cycle and growth2. Programmed cell death3. Cell-cell and cell-matrix adhesion4. Developmental signaling5. Allorecognition and innate
immunity6. Specialization of cell types
Some essential controls on the cell cycle evolved when animals first appeared
A-P patterning, Hox complex
A-P patterning Hox complex
Most signaling pathway and transcription factor families, intron-exon structure, genome organization
Early animal genomes are (in some ways) more similar to our genome than are the genomes of flies and nematodes
CNIDARIANSPLACOZOANSSPONGES BILATERIANS
Metazoan “toolkit”
A-P patterning Hox complex
Most signaling pathway and transcription factor families, intron-exon structure, genome organization
CNIDARIANSPLACOZOANSSPONGES BILATERIANS
Explanations for differences in complexity
microRNAs? cis-regulation?larger families?
Differences in the numbers of some types of genes do correlate with complexity
A-P patterning Hox complex
Most signaling pathway and transcription factor families, intron-exon structure, genome organization
CNIDARIANSPLACOZOANSSPONGES BILATERIANS
Cell types patterned in complex ways?
microRNAs? cis-regulation?larger families?
Explanations for differences in complexity
Summary
Animals evolved a “toolkit” of genes very early in their evolution
Early animal genomes are complex!(as are these animals)
Though not all questions are answered by the genomes, they are essential tools for finding the
remaining answers
Acknowledgements
Dan RokhsarNik Putnam, Oleg SimakovJarrod Chapman, Emina BegovicTherese Mitros, Uffe Hellsten
Heather Marlow and Mark Martindale (U. Hawaii)Kai Kamm, Michael Eitel, Bernd Schierwater (Hanover)Ana Signorovitch, Maria Moreno, Leo Buss, Stephen Dellaporta (Yale)Degnan group (U. Queensland), Kosik group (UC Santa Barbara)
Peter Reddien
Jessica Witchley, Kathleen MazzaMembers of the Reddien Lab
Ulf Jondelius, Swedish Museum of Natural HistoryWolfgang Sterrer, Bermuda Natural History Museum