1. Comparative Genomics

2. Overview Orthologues and paralogues Protein families
Genome-wide DNA alignments
Syntenic blocks

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

4. Species in Ensembl MAMMALS BIRDS REPTILES FISHES
CAMBRI ORDO SIL DEV CARBON PER TRIA JURA CRETAC TERTIA
570
505
438
408
360
286
245
208
144 65
MYBP
MAMMALS
PLACENTALS
MONOTREMES
MARSUPIALS
OTHER BIRDS
BIRDS
PALEOGNATHS
REPTILES
PASSERINES
CROCODILES
TURTLES
LIZARDS
AMPHIBIANS
TELEOSTS
FISHES
SHARKS
RAYS
LATIMERIA
BICHIR/POLYPTERUS
LUNGFISHES
AGNATHANS
NON-VERTEBRATES

5. Orthologue / Paralogue Prediction Algorithm
(1) Load the longest translation of each gene from all species used in Ensembl.
(2) Run WUBLASTp+SmithWaterman 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 PHYML. An unrooted tree is obtained at this stage.
(7) Reconcile each gene tree with the species tree to call duplication event on internal nodes and root the tree, using RAP.
(8) From each gene tree, infer gene pairwise relations of orthology and paralogy types.

6. 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

7. Orthologue and Paralogue Types

8. Orthologue and Paralogue types

9. GeneView

10. GeneView

11. GeneTreeView
MUSCLE
protein alignment
GeneTree

12. GeneTreeView
Speciation node (blue)
Duplication node (red)

13. Protein Dataset More than 1,500,000 proteins clustered:
All Ensembl protein predictions from all species supported
~ 670,000 protein predictions
All metazoan (animal) proteins in UniProt:
~ 80,000 UniProt/Swiss-Prot
~ 830,000 UniProt/TrEMBL

14. Clustering Strategy BLASTP all-versus-all comparison Markov clustering
For each cluster:
Calculation of multiple sequence alignments with ClustalW
Assignment of a consensus description

15. GeneView / TransView / ProtView
Link to FamilyView

16. FamilyView Consensus annotation JalView multiple alignments
Ensembl family members within human
UniProt family members
Ensembl family members in other species

17. JalView

18. 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

19. Selection of Species for DNA comparisons
Both coding and non-coding sequences
~70-75%
~150 MYA
4.2
Opossum
0.4
2.5
3.0
Size (Gbp)
~65%
~80%
>99%
Sequence conservation (in coding regions)
Primarily coding sequences
Recently changed sequences and genomic rearrangements
Aids identification of…
~450 MYA
~ 65 MYA
~5 MYA
Time since divergence
Pufferfish
Mouse
Chimpanzee
Human vs..

20. Alignment Algorithm
Should find all highly similar regions between two sequences
Should allow for segments without similarity, rearrangements etc.
Issues
Heavy process
Scalability, as more and more genomes are sequenced
Time constraint

21. 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
7 eutherian mammals
10 amniota vertebrates

22. BLASTZ-net, tBLAT and PECAN
For which combinations of species whole genome alignments have been done is shown on the Comparative Genomics page
(Help & Documentation > Genomic Data > Comparative Genomics):

23. ContigView Constrained elements Conservation score PECAN alignments
Blastz mouse
tBLAT zebrafish

24. MultiContigView
Conserved sequences human
Conserved sequences dog

25. AlignSliceView
Human
Mouse
Dog
Rat

26. MultiContigView vs. AlignSliceView

27. AlignView

28. GeneSeqalignView

29. GeneSeqalignView

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

31. SyntenyView Human chromosome Orthologues Mouse chromosomes

32. CytoView
Syntenic blocks
Orientation
Chromosome

33. Q
& A
Q U E S T I O N S
A N S W E R S