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Comparative Genomics
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Overview

• Orthologues and paralogues
• Protein families
• Genome-wide DNA alignments
• Syntenic blocks

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Comparative Genomics

• Tells us what is common and what is unique
  between different species at the genome level
• Allows us to achieve a greater understanding of
  vertebrate evolution
• The function of human genes and other regions may
  be revealed by studying their counterparts in
  lower organisms
• Helps us identify both coding and non-coding
  genes and regulatory elements

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Species in Ensembl
PLACENTALS
MAMMALS
MONOTREMES
MARSUPIALS
OTHER BIRDS
BIRDS
PALEOGNATHS
REPTILES
PASSERINES
CROCODILES
TURTLES
LIZARDS
AMPHIBIANS
TELEOSTS
FISHES
SHARKS
RAYS
LATIMERIA
BICHIR/POLYPTERUS
LUNGFISHES
AGNATHANS
NON-VERTEBRATES
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Homologue Relationships

• 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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Orthologue and Paralogue Types
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Orthologue and Paralogue Types
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Orthologue / Paralogue Prediction Algorithm

• (1) Load the longest translation of each gene
  from all species used in Ensembl.
• (2) Run WUBLASTpSmithWaterman of every gene
  against every other (both self and non-self
  species) in a genome-wise manner.
• (3) Build a graph of gene relations based on Best
  Reciprocal Hits (BRH) and Blast Score Ratio (BSR)
  values.
• (4) Extract the connected components (single
  linkage clusters), each cluster representing a
  gene family.
• (5) For each cluster, build a multiple alignment
  based on the protein sequences using MUSCLE.
• (6) For each aligned cluster, build a
  phylogenetic tree using TreeBeST using the CDS
  back-translation of the protein multiple
  alignment from the original DNA sequences. A
  rooted tree with internal duplication tags is
  obtained at this stage, reconciling it with the
  species tree.
• (7) From each gene tree, infer gene pairwise
  relations of orthology and paralogy types

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• Find the Ensembl F8 (coagulation factor VIII)
  gene of human and go to its GeneView page.
• Are there any within-species paralogues predicted
  for this gene?
• Is there an orthologue predicted for this gene in
  mouse?
• Retrieve an alignment between the human and mouse
  gene on both nucleotide and peptide level.
• Have a look at the genetree for this gene (hint
  have a look at the side menu when in GeneView).
• Can you identify the duplication event that gave
  rise to the two human paralogues?

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Clustering Strategy

• BLASTP all-versus-all comparison of
• all Ensembl protein predictions
• all metazoan (animal) proteins in UniProt
• Markov clustering
• For each cluster
• calculation of multiple sequence alignments with
  ClustalW
• assignment of a consensus description

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• FamilyView

JalView multiple alignments
Consensus annotation
E! family members within human
UniProt family members
Family members in other E! species
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• JalView

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Whole Genome Alignments

• Functional sequences evolve more slowly than
  non-functional sequences, therefore sequences
  that remain conserved may perform a biological
  function.
• Comparing genomic sequences from species at
  different evolutionary distances allows us to
  identify
• Coding genes
• Non-coding genes
• Non-coding regulatory sequences

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Selection of Species for DNA comparisons
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BLASTZ-net, tBLAT and PECAN

• BLASTZ-net (comparison on nucleotide level) is
  used for species that are evolutionary close,
  e.g. human - mouse
• Translated BLAT (comparison on amino acid level)
  is used for evolutionary more distant species,
  e.g. human - zebrafish
• PECAN is used for multispecies alignments, from
  which conservation scores and constrained
  elements are calculated
• 7 eutherian mammals
• 10 amniota vertebrates

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• Find the Ensembl BRCA2 (Breast cancer type 2
  susceptibility protein) gene for human and go to
  its ContigView page.
• Have a look at the conserved sequences with mouse
  and zebrafish. Which parts of the BRCA2 gene show
  the highest conservation? With which species is
  the conservation the highest, mouse or zebrafish?
  
• Have a look at the conservation score and
  constrained elements.

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• AlignSliceView

human
mouse
dog
rat
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• MultiContigView vs. AlignSliceView

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• Find the Ensembl A1bg (alpha-1-B glycoprotein)
  gene for mouse.
• Retrieve the genomic sequence alignment between
  the mouse and rat A1bg gene
• (hint have a look at the side menu when in
  GeneView).

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Syntenic Blocks

• Genome alignments are refined into larger
  syntenic regions
• Alignments are clustered together when the
  relative distance between them is less than 200
  kb and order and orientation are consistent
• Any clusters less than 100 kb are discarded

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• SyntenyView

Human chromosome
Mouse chromosome
Mouse chromosome
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• CytoView

Syntenic blocks
orientation
chromosome
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Q

A
Q U E S T I O N S A N S W E R S