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COMPARITIVE
GENOMICS.
GENOME.
• The whole genetic complement of an organism
• The study of all the genes present in an organism
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
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.
LIBRARIES
• Genomic Libraries:
• libraries of whole genome
• cDNA Libraries:
• libraries of only coding
regions (genes encodes for
some proteins)
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
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
• .
COMPARATIVE GENOMICS.
By comparing genomes of different
organisms we can find:
What is conserved between species
What make the closely related species
different
we can also study evolutionary changes,
gene function and inherited diseases
HOW TO COMPARE? Three possible ways to compare genomes
comparing of general features
Finer-Resolution comparison
Comparison of discrete segments
GENERAL FEATURES
• General features of genomes are comared to find
similarity and differences
• Genome Length
• Number of Exons
• Number of genes
• Chromosome Numbers
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
COMPARING OF DISCRETE SEGMENTS
Comparison of Discrete segments can be obtain through the
comparison of homologous segments of sequences for instance
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).
Applications Comparative genomics are used in finding
Evolutionary relationship
Counterparts of genes
New model organisms
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
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
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
Sparrow
Crow
Dove
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
STRUCTURE OF TREE
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
ClustalW2
Retriev sequence from NCBI and insert it into
ClustalW2 and submit it
RESULTS.
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
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
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.
INTRODUCTION TO GENOMES WITH
ENSEMBL
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.
Ensembl is Used Worldwide
Top users: UK US Canada China
France Germany Italy Japan Spain
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
Different species
whose genomes are
present in Ensemble
Total almost 69
spices
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
SEQUENCE DISPLAYS.
Gene: Sequence
Transcript:cDNA
Transcript: Exons
KARYOTYPE OF
HUMAN GENOME.
Chromosome Summary
Comparative Genomics
COMPARATIVE GENOMICS
• In comparative genomics section it provide four
options
• Alignment image
• Alignment Text
• Region comparison
• Synteny
ALIGNMENT IMAGE. • It show the image of alignment that at which
point which gene is similar to which
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
Human sequence is aligned against Mus
musculus specie
REGION COMPARISON
• It will compare different regions like protein
coding region, pseudo gene, RNA gene,
processed transcript etc.
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.
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
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.
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.
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.
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.
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
SEQUENCE IDENTITY
Coding regions showed strong sequence similarity, with
approximately 85%
In contrast, introns showed only weak sequence similarity
with approximately 35% sequence identity, which is not much
higher than the background rate of sequence identity in gapped
alignments of random sequences.
Coding regions showed strong sequence similarity,
with
approximately 85%
In contrast, introns showed only weak sequence
similarity
with approximately 35% sequence identity, which
is not much
higher than the background rate of sequence
identity in gapped
alignments of random sequences.
SEQUENCE IDENTITY
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