Transcript Slide 1

Comparative Genomics
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Overview of the Talk
• Comparing Genomes
• Homologies & Families
• Sequence Alignments
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Evolution at the DNA Level
Deletion
Mutation
…ACTGACATGTACCA…
Sequence edits
…AC----CATGCACCA…
Rearrangements
Inversion
Translocation
Duplication
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Why Compare Genomes?
• We can better understand evolution/
speciation
• We can find important, functional regions of
the sequence (codons, promoters, regulatory
regions)
• It can help us locate genes in other species
that are missing or not well-defined (also
through comparison and alignments).
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Comparing Genomes
 Mammals have roughly 3 billion base pairs in their
genomes
 Over 98% human genes are shared with primates,
wth more than 95-98% similarity between genes.
 Even the fruit fly shares 60% of its genes with
humans! (March 2000)
 Differences: gene structure, sequence
Remember… one nucleotide change can cause
disease such as sickle cell anemia and cancer.
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How Does Ensembl Predict
Homology?
• Uses all the species
• Uses a representative protein (the longest)
for every gene
• Builds a gene tree
•
EnsemblCompara GeneTrees: Analysis of complete, duplication aware
phylogenetic trees in vertebrates. Vilella AJ, Severin J, Ureta-Vidal A,
Durbin R, Heng L, Birney E. Genome Res. 2008 Nov 24.
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Steps in Homology Prediction
..MEDPATA…
Load longest protein for every
gene from all species
WU Blastp + SmithWaterman
longest translation of every gene
against every other
(Blast Reciprocal Hit/ Blast Score Ratio)
Protein clustering, build multiple
alignments (MCoffee)
From each alignment,
build a gene tree
Reconcile each gene tree with the
species tree to determine internal
nodes (TreeBest)
Orthologues, paralogues…
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Viewing Trees in Ensembl
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Types of Homologues
• Orthologues : any gene pairwise relation
where the ancestor node is a speciation event
• Paralogues : any gene pairwise relation where
the ancestor node is a duplication event
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The Gene Tree for INS
(insulin precursor)
A blue square
is a
speciation
event
(Orthologues)
A red square
is a
duplication
event
(Paralogues)
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Reconciliation
M
M
Duplication node
Speciation node
R
R
H
species tree
H
M
M
R’
H
H
H’
R
unrooted gene tree
M’
R
Orthologue Types
What is ‘1 to 1’?
What is ‘1 to many’?
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Protein Families
• How: Cluster proteins for every isoform
in every species + UniProt proteins.
• BLASTP comparison of:
– all Ensembl ENSP…
– all metazoan (animal) proteins in UniProt
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Homologues Exercise
1. Find the human MYL6 gene: go to
its gene summary.
2. How many paralogues does it
have? Find them in the gene tree.
3. Which paralogue is closest to the
human MYL6 gene? In what taxon
is the common ancestor?
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Pan-Compara (Ensembl Genomes)
x2
x8
Bacillus subtilis
Escherichia coli K12
Mycobacterium tuberculosis H37Rv
Neisseria meningitidis A 4A
Pyrococcus horikoshii
Staphylococcus aureus N315
Streptococcus pneumoniae TIGR4
Streptococcus pyogenes M1 SF370
Plasmodium falciparum
Plasmodium vivax
x2
Saccharomyces cerevisiae
Schizosaccharomyces pombe
x3
Arabidopsis thaliana
Oryza sativa japonica
Vitis vinifera
x3
Anopheles gambiae
Caenorhabditis elegans
Drosophila melanogaster
x13
Anolis carolinensis
Ciona savignyi
Danio rerio
Equus caballus
Gallus gallus
Homo sapiens
Macaca mulatta
Monodelphis domestica
Mus musculus
Ornithorhynchus anatinus
Pan troglodytes
Pongo pygmaeus
Xenopus tropicalis
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www.ensemblgenomes.org
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Families
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Ensembl Proteins in the Family
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Overview of the Talk
• Comparing Genomes
• Homologies and Families
• Sequence Alignments
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Non-Coding Regions
• Large stretches of non-coding regions in
vertebrates
• Regulatory regions of:
Developmental genes
Transcription factors
miRNA
Kikuta et. al, Genome Research, May 2007
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Comparative Genomics
today
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Aligning Whole Genomes- Why?
• To identify homologous regions
• To spot trouble gene predictions
• Conserved regions could be functional
• To define syntenic regions (long regions of
DNA sequences where order and orientation is
highly conserved)
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Aligning large genomic sequences
Difficulties:
• Requires a significant computer resource
• Scalability, as more and more genomes are
sequenced
• Time constraint
• As the «true» alignment is not known, then
difficult to measure the alignment accuracy
and apply the right method
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Whole Genome Alignments
• BLASTZ-net (nucleotide level)
closer species e.g. human – mouse
• Translated BLAT (amino acid level)
more distant species, e.g. human – zebrafish
• EPO/PECAN multispecies alignments
• ORTHEUS used to determine ancestral alleles
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Alignments Exercise
1. Find the Ensembl MYH2 gene for
human and go to Region in Detail.
2. Turn on the BLASTZ alignment against
cow. What part of the cow genome
aligns to this region in human?
3. Jump to the region in cow.
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Alignments Exercise
Go back to the human page.
•
Use the Alignments (text) and
Multi-species view links to explore
the alignments.
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Conserved Regions Exercise
Go back to region in detail
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Turn on the conservation score for 31
species, and the constrained elements tracks.
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Where are the regions of high conservation?
1. Click on the regulatory feature that
corresponds to a highly conserved block of
sequence. What is it?
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Ancestral Alleles
• Go to the variation tab for rs34161789,
and take the Phylogenetic Context link.
• What is the allele in the four primates?
Hint… either go to the gene tab and click on
the SNP ID from the variation table, or do
a new search using rs34161789.
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Compara Team at EBI
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Javier Herrero
Kathryn Beal
Stephen Fitzgerald
Albert Vilella
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End of Course Survey
Exercises on page 43. Answers are on page 44.
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