This is the third presentation of the BITS training on 'Comparative genomics'. It reviews the basic concepts of sequence homology on the gene Thanks to Klaas Vandepoele of the PSB department.

1. Comparative genomics
in eukaryotes
Genome analysis
Klaas Vandepoele, PhD
Professor Ghent University
Comparative & Integrative Genomics
VIB – Ghent University, Belgium

2. I. Genome conservation & genomic
homology
 Alignment of homologous regions
 Inter-genomic: aligning genomic sequences from different
species
 Intra-genomic aligning genomic sequences from the same
species
 Different levels of resolution
 Comparative mapping (markers)
 Synteny (~ gene content)
 Colinearity (gene content + order conservation)
 DNA-based alignments (base-to-base mapping)
2

3. Human – Mouse - Rat
resolution
3

4. Human – Mouse orthologous
regions resolution
Genome translocations associated
Comparative
with human-mouse speciation
mapping
Human
Mouse chr IV
4 www.ensembl.org

5. Human genome browser
resolution
Conserved gene Human chr I
content & order Mouse chr IV
Gene loss and insertions in orthologous
segments since human-mouse speciation
EST/cDNA
similarities
Genome
similarities
5 Human gene model

6. Human – Mouse base-to-base
mapping resolution
 Functional sequences
(e.g. exons) evolve slower
than non-functional ones
(e.g. introns) due to
natural selection against
mutations in these regions
 Consequently,
functional elements, both
coding and non-coding,
are unusually well
conserved in orthologous
regions
Blue: coding exons GT donor AG acceptor
6

7. DNA substitution rates for different
gene/genome regions
7 Molecular Evolution, Li WH

8. Multiple species comparisons
(gene-based)
8 Hedges, 2002 PhIGs

9. Genome size variation in the grasses:
the use of model systems
BEP Rice 450Mb
46 MYA
55 MYA Barley ~5000Mb
28 MYA
PACC Sorghum ~750Mb
Maize ~2400Mb
9 Gaut 2002

10. Grass genomes: a single genetic
system?
Gale and Devos, 1998
10

11. Micro-colinearity within the grasses
11 Bennetzen lab

12. Yeast Gene Order Browser (YGOB)
12

13. II. Computational detection of
genomic homology
 Synteny
~ conservation of gene content
 Colinearity
~ conservation of (gene) content & order
 Macro-colinearity
 Marker-based
 Micro-colinearity
 DNA based or gene-based
13

14. How to find evidence for gene
colinearity?
A 1 2 3 4 5 6 7 8 9 10 11
speciation
S1 1 2 3 4 5 6 7 8 9 10 11
S2 1 2 3 4 5 6 7 8 9 10 11
Time
Gene loss, insertions,
rearrangements,
translocation, etc …
2
S1 1 3 4 6 7 10 11
S2 1 2 4 6 7 8 9 11
retained orthologs (anchor points)
14

15. Matrix representation
S1 1 3 4 6 7 10 11
S2 1 2 4 6 7 8 9 11
segment S1
1 - 3 4 - 6 7 X X 10 11
1
2
-
segment S2
4
X
6
7
8
9
-
15 11

16. Map-based approach
Chromosome 1
• Represent chromosomes
as sorted gene lists
• Identify all homologous
Chromosome 2
gene pairs between
chromosomes (all-
against-all BLASTP*).
• Score pairs of
homologues in matrix
Identifying homologous regions = identifying diagonal series of
elements in the gene homology matrix (GHM).
16 Vandepoele et al., Genome Research 2002

17. The map-based approach: terminology
Chromosome 1
Colinear segment
Tandem duplication
Chromosome 2
Homologous gene
Inverted colinear segment
1
2
Gene Homology Matrix (GHM)
17

18. Detection of colinear homologous
regions
Human-mouse Chicken-human
MmuC4
HsaC1
HsaC1 GgaC23
18

19. Detection of colinear homologous
regions
Human-mouse Human-tetraodon
MmuC4
TviC1
HsaC1 HsaC1
19

20. MUMmer
NUCmer PROmer
20

21. And what about synteny?
HsaC1
• Application of 2-
dimensional sliding-
HsaC9
window approach to
score regions with a high
density of homologous
genes between 2
chromosomes
ancient duplication
Identifying syntenic regions = identifying high homolog-density
regions in the gene homology matrix (GHM).
21 DeSyRe, Vandepoele et al. unpublished

22. Detection of recent and ancient large-
scale duplications
recent duplication ancient duplication
C2 HsaC1
C4 HsaC9
22 colinearity synteny

23. III. Whole-genome alignments
 Evolutionary constrained sequences are a
good indicator of functional genome regions
 Basic protocol
1. Sequence generation
2. Reconstructing homologous colinearity across
related genomes
3. Multi-sequence alignment
4. Detection sequences under purifying selection.
23 Margulies & Birney, NRG 2008

24. Reconstructing homologous
colinearity
• Segmental duplication and other species-specific
rearrangements (e.g. inversions, insertions, deletions)
interfere with the accurate detection of orthologous
genomic regions
24

25. Tools
 Mercator (Ensembl)
 coding exons as anchor points
 graph of colinearity information
 travel through graph to generate homologous
regions
 chains-and-nets (UCSC)
 reference-based local alignments different
genomes (BLASTZ)
 filtering highest-scoring chains
 net together chains from same locus
25

26. Sequence alignment & constraint
detection
PhastCons
BinCons
GERP
Siphy
26

27. Whole-genome base-pair
alignment
 Challenges
 multi-species alignment
 long DNA sequences (reflecting homologous
colinear regions)
 one-to-one mapping (with reference genome)
 various levels of sequence divergence
27

28. Whole-genome base-pair
alignment toolbox
 MLAGAN
 CHAOS seeding algorithm (k-mer anchors)
 Dynamic programming (pairwise)
 Multiple alignment using progressive strategy
 Shuffle-LAGAN (incl. rearrangement map); VISTA
 TBA / MultiZ; UCSC
 Pairwise BLASTZ alignments (local blocks)
 Merging joining blocks using MultiZ
 Complex ordering of blocks using Threaded Blockset Aligner
 PECAN (Ensembl)
 Consistency alignment based on pairwise alignments (incl. outgroup
information)
 MAVID
28

29. From gene to DNA-based
colinearity…
Pairwise approach:
Human segment as
reference
29 VISTA
http://genome.lbl.gov/vista

30. From gene to DNA-based
colinearity…
30

31. Input and output files
PIP- maker
31 Frazer et al., 2003

32. Conserved Non-coding Sequences or
Elements (CNS/CNE)
Human/dog
Human/mouse
Mouse/dog
VISTA plot
Blue: exons
Turquoise: UTR
32

33. Exercise
 Explore the genome organization and
conservation of your favorite locus in a set of
related species.
 Plants
 http://bioinformatics.psb.ugent.be/plaza/
 Vertebrates
 http://teleost.cs.uoregon.edu/synteny_db/
 Yeast
 http://wolfe.gen.tcd.ie/ygob/
33

34. 34