Comparative genomics allows scientists to compare the genomes of different organisms to better understand genome structure and function. By aligning homologous genes, researchers can identify regions of similarity and difference between species that provide insights into evolution, gene function, and disease. The Ensembl database facilitates comparative genomic analyses across 69 vertebrate and eukaryotic species by allowing users to search for similar sequences, view alignments and gene trees, and integrate external genomic data. Comparisons between human and mouse genomes reveal approximately 85% identity in coding regions and gene structures but more divergence in intron sequences and lengths.

1. COMPARITIVE
GENOMICS.

2. GENOME
.
• The whole genetic complement
of an organism
• The study of all the genes present
in an organism

3. WHAT IS THE GENOME.
• cells contain chromosomes.
• Chromosomes consist of million of
genes.
• All these genes are present in DNA.
• The four Nucleotides(A,G,C,T) arrange
in different combinations to form
different genes.
• DNA encodes for thousands of proteins.
• Hereditary material

4. DNA SEQUENCING
• DNA of any organism is sequenced in
parts.
• In DNA sequencing both Molecular
biology and Computational techniques
is used.
• Molecular biology techniques like
Recombinant DNA Technology, PCR
amplification, Libraries Constructions
etc are used.
• Ultimately DNA Libraries are
constructed.

6. LIBRARIES
• Genomic Libraries:
• libraries of whole genome
• cDNA Libraries:
• libraries of only coding
regions (genes encodes for
some proteins)

7. SEQUENCED GENOMES
• After the completion of Human Genome
Sequencing in 2001 , genomes of many other
organisms are sequenced
• Table below show few examples of organisms
whose genomes are sequenced
Organisms
Year
Scientist
mouse
2002
Waterston et al
rat
2005
Gibbs et al
fruit fly
2000
Adams et al
baker's yeast
1996
Goffeau et al.
chicken
2004
Blattner et al
cow
2009
Elsik et al.
monkey
2007
Gibbs et al

8. COMPARATIVE GENOMICS
•
comparative genomics is the field of biology in which
genomes of different organisms are compared by using
computational techniques
•
Sequence alignment is main principle on which field of
comparative genomics based
•
•
Different techniques of sequence alignment are in used
Dot Plot
•
Dynamic Programming
• Smith waterman algorithm
• Needleman Wunch Algorithm
Heuristics
• FASTA,
• BLAST etc
.
•
•

9. COMPARATIVE GENOMICS.
 By comparing genomes
organisms we can find:
of
different
 What is conserved between species
 What make the closely related species
different
 we can also study evolutionary changes,
gene function and inherited diseases

10. HOW TO COMPARE?
 Three possible ways to compare genomes
comparing of general features
Finer-Resolution comparison
Comparison of discrete segments

11. GENERAL FEATURES
• General features of genomes are comared to find
similarity and differences
•
•
•
•
Genome Length
Number of Exons
Number of genes
Chromosome Numbers

13. FINER RESOLUTION METHOD.
In Finer-Resolution Method genomes are compared by the direct
comparison of DNA sequences of different species for instance
Human chromosomes, with segments containing at least two
genes whose order is conserved in the mouse genome as colour
blocks. Each colour corresponds to a particular mouse
chromosome. Centromeres, subcentromeric heterochromatin of
chromosomes 1, 9 and 16, and the repetitive short arms of 13, 14,
15, 21 and 22 are in black.
Conserved segments in the human and mouse genome

14. COMPARING OF DISCRETE SEGMENTS
Comparison of Discrete segments can be obtain through the
comparison of homologous segments of sequences
instance
for
A human gene (pyruvate kinase: PKLR) and the corresponding PKLR homologs
from macaque, dog, mouse, chicken, and zebrafish are aligned. Macaque show
similarity in all regions like exon(blue),introns(red) and untranslated regions(light
blue).

15. Applications
 Comparative genomics are used in finding
Evolutionary relationship
Counterparts of genes
New model organisms

16. EVOLUTIONARY RELATIONSHIP
o With the passage of time some changes take
place in the hereditary materiel which sometime
brings useful changes and sometime cause
drastic effect
o To study these changes evolutionary trees are
generated on the bases of evolutionary distances
o Two types of trees are constructed
o Rooted trees
o Unrooted trees

17. ROOTED TREE
• Rooted Tree is that tree which show the common
ancestor of all the target organisms
EXAMPLE
• let suppose we say that Human, apes, gorillas are all
comes under the Mammals. So we can say that
mammals is the parent of all so it is a common ancestor
all

18. UNROOTED TREE
• Unrooted trees are those trees which show the relationship of target
organisms with each other but do not show the common ancestor of all
• EXAMPLE
• Let suppose we say that Eagle, Sparrow, Crow, Dove are all related to each
other some how
Eagle
Crow
Sparrow
Dove

19. TERMINOLOGIES.
• Some of the terminologies used is studying Phylogenatic trees
are
• Root:
• The point which represent the common ancestor of all target
organisms
• Nodes:
• Points from which leaves originates
• Leaves:
• The teminal nodes or the end children of the tree
• Clade:
• Subtree of a large tree

20. STRUCTURE OF TREE

21. SOFTWARES.
• The most commonly used software for
constructing the Phylogenatic tree is
ClustralW
• In clustralW insert all the sequences in it in
FASTA format
• Than submit it
• Select guide tree option to generate tree

22. ClustalW2
Retriev sequence from NCBI and insert it into
ClustalW2 and submit it

23. RESULTS.

24. COUNTER PARTS OF GENES
• Dramatic results have emerged from the
rapidly developing field of comparative
genomics
• Comparison of the fruit fly genome with the
human genome reveals that about sixty
percent of genes are conserved (Adams et al.
2000). That is, the two organisms appear to
share a core set of genes
• Researchers have also found that two-thirds
of human genes known to be involved in
cancer have counterparts in the fruit fly

25. CONT…
 Michigan Tech researchers Thomas Werner and Komal
Kumar Bollepogu Raja have traced these black spots to
three specific genes in the fruit fly genome. These
particular genes all have counterparts in human DNA,
and all three of these counterparts just so happens to
cause cancer.
 "We are looking here at proto-oncogenes, which are
cancer genes that cause disease when they are active in
an uncontrolled manner. Both humans and flies have
them, and in flies they learned to paint black spots on the
abdomen

26. MODEL ORGANISMS
 Comparative genomics is an exciting new field of biological
research in which the genome sequences of different
species - human, mouse and a wide variety of other
organisms from yeast to chimpanzees - are compared.
 By comparing the finished reference sequence of the
human genome with genomes of other organisms,
researchers can identify regions of similarity and
difference. This information can help scientists better
understand the structure and function of human genes and
thereby develop new strategies to combat human diseases
 when scientists inserted a human gene associated with
early-onset Parkinson's disease into fruit flies, they
displayed symptoms similar to those seen in humans with
the disorder, raising the possibility the tiny insects could
serve as a new model for testing therapies aimed at
Parkinson's.

27. INTRODUCTION TO GENOMES WITH
ENSEMBL

28. DATABASE OF COMPARATIVE
GENOMICS.
 Ensemble is a database in which genomes of different
vertebrates and eukaryotes are store
 By using Ensemble one can use BLAST and BLAT to
search the similar sequences in other species and
organisms
 User can download sequences in FASTA format and
can also view the karyotypes
 One can find Homologues, gene trees, and whole
genome alignments across multiple species.
 User can get information about DNA methylation,
transcription factor binding sites, histone
modifications, and regulatory features such as
enhancers and repressors, and microarray
annotations.

30. Ensembl is Used Worldwide
Top users: UK US Canada China
France Germany Italy Japan Spain

31. THE ENSEMBL GENOME BROWSER:
MAKING IT INTERESTING
 Splice variants, proteins, non-coding RNA
 Small and large scale sequence variation, phenotype
associations
 Whole genome alignments, protein trees
 Potential promoters and enhancers, DNA methylation
 User upload, custom data

32. Different
species
whose genomes are
present in Ensemble
Total almost 69
spices

33. ENSEMBL FEATURES
 The gene set.
 •Comparative analysis
 •Variation and regulation
 •BioMart (data export)
 •Display of external data
(DAS) •Programmatic
access via the Perl API.
 •Open Source

34. SEQUENCE DISPLAYS.
Transcript:cDNA
Gene: Sequence
Transcript: Exons

35. KARYOTYPE OF
HUMAN GENOME.

36. Chromosome Summary

37. Comparative Genomics

38. COMPARATIVE GENOMICS
•
In comparative genomics section it provide four
options
• Alignment image
• Alignment Text
• Region comparison
• Synteny

39. ALIGNMENT IMAGE.
• It show the image of alignment that at which
point which gene is similar to which

40. ALIGNMENT TEXT
• It give the whole sequence in FASTA format
in which Exons are highlighted
• It also provide an opportunity of alignment
• User can select the specie to which he/she
want to align the target sequence
• The results will show all possible hits of the
target sequence or region in that specie
• Chromosome number and position of the
similar region on it are provided for all hits
• One can check its detail by selecting it

41. Human sequence is aligned against Mus
musculus specie

42. REGION COMPARISON
• It will compare different regions like protein
coding region, pseudo gene, RNA gene,
processed transcript etc.

43. SYNTENY..
In classical genetics, synteny describes
the physical co-localization of genetic
loci on the same chromosome within an
individual or species.
It show the similar region in the form of
bands of different colors.

44. HUMAN VS MOUSE..
• Human
and
mouse
genome
show
approximately 85% identity
• Comparisons of mRNA sequences of 1196
orthologous human and mouse gene pairs were
recently reported (Makalowski et al. 1996),
showing that coding regions tend to show
approximately 85% identity at the nucleotide
and protein levels
• A total of 117 orthologous gene pairs were
identified and studied

45. Exon Identity..
• For the purpose of comparing the genomic structure of the
gene pairs, we used dynamic programming algorithms
(employing both nucleotide similarity and codon
similarity using the PAM20 matrix (Dayhoff et al. 1978))
to align the sequences. We carefully inspected the
alignments to ensure that they correctly aligned the exons.
• The number of exons was identical for 95% of the genes
studied. There were six instances in which the number of
exons differed.

46. CONT….
• In two cases, a single internal coding exon in
mouse is reported to correspond to two internal
coding exons in human. In the spermidine
synthase gene, mouse exon 5 corresponds to
human exons 5 and 6, with the total exonic
lengths agreeing perfectly
• In the lymphotoxin beta gene mouse exon 2
corresponds to human exons 2 and 3.
Interestingly, the mouse exon 2 is 316 bp while
the sum of the lengths of human exon 2, intron
2 and exon 3 is only 301 bp.

47. EXON LENGTH
 The length of corresponding exons was strongly conserved.
The lengths were identical in 73% of cases. Those differences
that did occur were quite small: the mean ratio of the larger to
smaller length was 1.05.
 Moreover, the differences were nearly always a multiple of
three. The length difference was a multiple of three for 95% of
all exons and 99% of all internal coding exons. This is readily
understood in terms of the effects of evolutionary selection
 Only three instances were found in which corresponding
internal exons had lengths differing by other than a multiple of
three.

48. CONT..
o In the skeletal muscle specific myogenic gene the
respective lengths of exons 2 and 3 are 81 bp and 123 bp
in the human and 82 and 122 in the mouse
o gene encoding the Flt3 ligand The respective lengths of
exons 2 and 3 are 111 bp and 54 bp in the human and
122 bp and 46 bp in the mouse, while the respective
lengths of exons 5 and 6 are 139 bp and 179 bp in the
human and 144 bp and 189 bp in the mouse.

49. Intron length
 Exon lengths tended to be well-preserved,
intron lengths varied considerably
 Human introns tended to be larger than mouse
introns (68% of cases), but this could represent
a selection bias reflecting the fact that the less
extensive sequencing of the mouse genome
may lead to an underrepresentation of instances
in which the mouse genomic locus is larger

50. SEQUENCE IDENTITY
SEQUENCE IDENTITY
Coding regions showed strong sequence similarity,
with
approximately 85%

Coding regions showed strong sequence similarity, with
In approximately 85%
contrast, introns showed only weak sequence
similarity
with approximately 35% sequence identity, which
is
 not much
In contrast, introns showed only weak sequence similarity
higher than the background rate of sequence
with approximately 35% sequence identity, which is not much
identity in gapped
alignments of the background rate of sequence identity in gapped
higher than random sequences.
alignments of random sequences.

51. SEQUENCE IDENTITY
• The degree of conservation varied considerably
among genes. For example, the gene encoding the
ribosomal protein S24 showed 88% identity at the
DNA level and 100% identity at the amino acid level
in coding exons, but only 27% identity at the DNA
level in introns.
• In the tumor necrosis factor-beta gene the first intron
has 75% nucleotide identity and nearly perfect
agreement in length (86 bp in human, 83 bp in
mouse). Interestingly, the flanking exons are less
well-conserved, showing only 70% nucleotide
identity and 60% amino acid identity