Comparative genomics

Presented by Arooba Baig Fomaz Tariq

GenomicsGenomics is an area within genetics that concerns the sequencing and analysis of an organism’s

genome.Development and application of genetic mapping, sequencing, and computation (bioinformatics) to

analyze the genomes of organisms.

Sub-fields of genomics:

Structural genomics-genetic and physical mapping of genomes.

Functional genomics-analysis of gene function (and non-genes).

Comparative genomics-comparison of genomes across species.

Includes structural and functional genomics.

Evolutionary genomics.

Comparative genomicsComparative genomics is an exciting field of biological research in which

researchers use a variety of tools, including computer-based analysis, to compare the complete genome sequences of different species

A comparison of gene numbers, gene locations & biological functions of gene, in the genomes of different organisms, one objective being to identify groups of genes that play a unique biological role in a particular organism.

History•  Comparative genomics has a root in the comparison of virus genomes in

the early 1980s.• For example, small RNA viruses infecting animals (picorna viruses) and

those infecting plants ( cowpea mosaic virus) were compared and turned out to share significant sequence similarity and, in part, the order of their genes.

• In 1986, the first comparative genomic study at a larger scale was published, comparing the genomes of varicella-zoster virus and Epstein-Barr virus that contained more than 100 genes each

Contd..• The first complete genome sequence of a cellular organism, that of

Haemophilus influenzae Rd, was published in 1995. • The second genome sequencing paper was of the small parasitic

bacterium Mycoplasma genitalium published in the same year. • Saccharomyces cerevisiae, the baker's yeast, was the first eukaryote

to have its complete genome sequence published in 1996.• After the publication of the roundworm Caenorhabditis elegans genome

in 1998, and together with the fruit fly Drosophila melanogaster genome in 2000, Gerald M. Rubin and his team published a paper titled "Comparative Genomics of the Eukaryotes“.

• In which they compared the genomes of the eukaryotes D. melanogaster, C. elegans, and S. cerevisiae, as well as the prokaryote H. influenza .

Related Terminologies• Homology is the relationship of any two characters (such as two proteins that have similar

sequences) that have descended, usually through divergence, from a common ancestral character

• Homologues Homologues can either be orthologues, paralogues

• Orthologues are homologues that have evolved from a common ancestral gene by speciation. They usually have similar function

• Paralogues are homologues that are related or produced by duplication within a genome. They often have evolved to perform different functions

Comparative Genomics Tools Similarity search programs • BLAST2 (Basic Local Alignment Search Tool) • FASTA • MUMmer (Maximal Unique Match) (Comparisons and analyses at both Nucleic

acid and protein level) Other alignment programs • DBA [DNA Block Aligner]• Blastz• BLAT/AVID, – WABA [Wobble Aware Bulk Aligner] • DIALIGN [Diagonal ALIGNment]• SSAHA [Sequence Search and Alignment by Hashing Algorithm]

Contd.. Comparative gene prediction programs Twins can Double scan SGP-1 Regulatory region prediction Consite Visualization/ Sequence analysis programs Dot plot (e.g. Dotter) PIP maker (Percent Identity Plot) Alfresco VISTA (VISualization Tools for Alignments) ACT (Artemis comparison tool) S S Jena

Comparative Genomics Tool The UCSC Genome Browser is an on-line genome

browser hosted by the University of California, Santa Cruz. The UCSC Genome Browser is an on-line genome browser hosted by the University of California, Santa Cruz

Synteny RegionsSynteny Regions of two genomes that show considerable similarity in

terms of sequence and conservation of the order of genes. Genes that are in the same relative position on two different

chromosomes. Closely related species generally have similar order of genes on

chromosomes. Synteny can be used to identify genes in one species based on map-

position in another

Interactive DAGchianer Algorithm:Tool for mining GenomeDuplication & Synteny

Finding putative genes or regions of homology between two genomes

Identifying collinear sets of genes or regions of sequence

Generating a dot plot of the results and coloring syntenic pairs.

Comparative Genomics Tool

Syntentic dot plot:  Syntentic dot plots give biologists very valuable information about how organisms diverged from a common ancestor. 

Biologists can easily look at one of these dot plots and see where large sections of DNA have been deleted, inserted, copied, or moved. 

The dot plots are also very good at depicting how closely two organisms are related through the quantity and linearity of green dots over an entire genome.

Sequence Similarity Search

The most frequently performed type of sequence comparison is the sequence similarity search

Sequence comparisons that implicate function are widely used: To determine if newly sequenced cDNA or genomic region encodes gene

of known function. Search for similar sequence in other species (or in same species)

Contd.. Search databases of DNA sequences Use computer algorithms to align sequences Don’t require perfect matches between sequences Most commonly used algorithms: BLAST FAST-A Homology searches

BLASTThe Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between

sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

General Databases Useful for Comparative Genomics

• Locus Link/Ref Seq: http://www.ncbi.nih.gov/LocusLink/ • PEDANT-Protein Extraction Description Analysis Tool http://pedant.gsf.de • COGs - Cluster of Orthologous Groups (of proteins) http://www.ncbi.nih.gov/COG/ • KEGG- Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg/ • MBGD - Microbial Genome Database http://mbgd.genome.ad.jp/ • GOLD - Genome Online Database http://wit.integratedgenomics.com/GOLD/ • TIGR – The Institute of Genome Research Comparative genomics of Parasites

Comparative genomic process

 Alignment of DNA sequences is the core process in comparative genomics.

An alignment is a mapping of the nucleotides in one sequence onto the nucleotides in the other sequence, with gaps introduced into one or the other sequence to increase the number of positions with matching nucleotides.

Several powerful alignment algorithms have been developed to align two or more sequences

Methods for comparative genomics

• Comparative analysis of genome structure• Comparative analysis of coding regions (exon)• Comparative analysis of non-coding regions (introns)

Comparative analysis of genome structure

Analysis of the global structure of genomes, such as nucleotide composition, syntenic relationships, and gene ordering offer insight into the similarities and differences between genomes.

This provide information on the organization and evolution of the genomes, and highlight the unique features of individual genomes

The structure of different genomes can be compared at three levels: • Overall nucleotide statistics,• Genome structure at DNA level• Genome structure at gene level.

Comparison of genome structure at DNA level

Chromosomal breakage and exchange of chromosomal fragments are common mode of gene evolution. They can be studied by comparing genome structures at DNA level.

• Identification of conserved Synteny and genome rearrangement events• Analysis of breakpoints• Analysis of content and distribution of DNA repeats

Comparison of genome structure at gene level

Chromosomal breakage and exchange of chromosomal fragments cause disruption of gene order

Therefore gene order correlates with evolutionary distance between genomes

Comparative analysis of coding regions

The analysis and comparison of the coding regions starts with the gene identification algorithm that is used to infer what portions of the genomic sequence actively code for genes.

There are four basic approaches for gene identification

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Comparative analysis of coding regions

Number of algorithms that have been use in comparative genomics to aid function prediction of genes.

Identification of gene-coding regions

comparison of gene content

comparison of protein content

Comparative genome based function prediction

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Comparison of gene content

After the predicted gene set is generated, it is very interesting and important to compare the content of genes across genomes

The first statistics to compare is the estimated total number of genes in a genome, elucidate the similarities and differences between the genomes include percentage of the genome that code for genes, distribution of coding regions across the genome average gene length, codon usage

This is often done using a pairwise sequence comparison tool such as BLASTN or TBLASTX

Comparison of protein contentA second level of analysis that can be performed is to compare the set of

gene products (protein) between the genomes, which has been termed ‘‘comparative proteomics”

It is important to compare the protein contents in critical pathways and important functional categories across genomes

Two widely used resources for pathways and functional categories are the KEGG pathway database and the Gene Ontology (GO) hierarchy

• Interesting statistics to compare include• Level of sequence identity between orthologous pairs across genome• Paralogous pairs within genome,• Number of replicated copies in corresponding paralog families• Functions of the paralogs

Comparative analysis of noncoding regions

Noncoding regions of the genome gained a lot of attention in recent years because of its predicted role in regulation of transcription, DNA replication, and other biological functions

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Insights into Genome Fluxes and the Processes of Evolution

• From an evolutionary biology perspective, whole genome comparisons provide molecular insights into the processes of evolution that include the molecular events responsible for the variations and fluxes that occur through a genome. These include processes like, inversions, translocations, deletions, duplications and insertions.

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The Impact of Comparative Genomics in Phylogenetic Analysis

Schematic depiction of Microsporidia's phylogenetic position based on Small Subunit RNA (SSU rRNA) as an early branching eukaryote that evolved prior to the acquisiton of mitochondria, and it's subsequent placement based on a composite gene phylogeny where it was placed closer to fungi. The latter placement has been confirmed by the complete sequenceof the micro-sporidia, Encephalitozoon cuniculi, where despite the absence of mitochondria, the presence of several mitochondrial genes could be observed.

Contd…We have learned from homologous sequence alignment that the information that

can be gained by comparing two genomes together is largely dependent upon the phylogenetic distance between them.

Phylogenetic distance is a measure of the degree of separation between two organisms or their genomes on an evolutionary scale, usually expressed as the number of accumulated sequence changes, number of years, or number of generations.

The more distantly related two organisms are, the less sequence similarity or shared genomic features will be detected between them.

Thus, only general insights about classes of shared genes can be gathered by genomic comparisons at very long phylogenetic distances (e.g., over one billion years since their separation). Over such very large distances, the order of genes and the signatures of sequences that regulate their transcription are rarely conserved

How Are Genomes Compared?

• A simple comparison of the general features of genomes such as genome size, number of genes, and chromosome number presents an entry point into comparative genomic analysis.

• Data for several fully-sequenced model organisms is shown in Table 1.

Contd…• For example, while the tiny flowering plant Arabidopsis thaliana has a

smaller genome than that of the fruit fly Drosophila melanogaster (157 million base pairs v. 165 million base pairs, respectively)

• It possesses nearly twice as many genes (25,000 v. 13,000). • In fact A. thaliana has approximately the same number of genes as

humans (~25,000). • Thus, a very early lesson learned in the "genomic era" is that genome

size does not correlate with evolutionary status, nor is the number of genes proportionate to genome size.

Contd..• Figure 1 depicts a chromosome-level comparison of the human and

mouse genomes that shows the level of Synteny between these two mammals

• Synteny is a situation in which genes are arranged in similar blocks in different species.

• The nature and extent of conservation of Synteny differs substantially among chromosomes.

• For example, the X chromosomes are represented as single, reciprocal syntenic blocks.

• Human chromosome 20 corresponds entirely to a portion of mouse chromosome 2, with nearly perfect conservation of order along almost the entire length, disrupted only by a small central segment

• Human chromosome 17 corresponds entirely to a portion of mouse chromosome 11.

• Other chromosomes, however, show evidence of more extensive interchromosomal rearrangement.

• Results such as these provide an extraordinary glimpse into the chromosomal changes that have shaped the mouse and human genomes since their divergence from a common ancestor 75–80 million years ago.

Comparing Human, Chimp, and Mouse Genomes

The graphs below indicate the similarity between the human genome and those of the chimpanzee and the mouse as they are mapped to identical locations in the human genome.

Since the chimpanzee genome is closer in evolutionary time to the human genome, the chimp chromosomes map very closely to human chromosomes

The mouse genome is more distant in evolutionary time from human, and thus its chromosomes do not map as closely as do the chimp chromosomes.

The white areas indicate areas of the human genome that either do not map well to the other genome, or are areas of centromeres and telomeres where the genome sequence is unknown.

Chromosome numbering is purely arbitrary, based upon early microscopic estimates of chromosome length.

The chimpanzee genome has 23 numbered chromosomes, the human genome has 22 numbered chromosomes (chimp chromosomes 2a and 2b map to human chromosome 2), the mouse genome has 19 numbered chromosomes.

The X and Y sex chromosomes have unique names, as well as other unique characteristics.

Mouse genome mapped on the human genome

• This image shows the 34% of the mouse genome that maps to identical sequence in the human genome.

• The matching locations are jumbled, indicating rearrangements of the two genomes since their last common ancestor, approximately 75 million years before present. 

• Data for this figure comes from assemblies of the human and mouse genomes available from the UCSC Genome Browser in June 2006.

Chimpanzee genome mapped on the human genome• This image shows the 95% of the

chimpanzee genome that maps to identical sequence in the human genome.

• The consistency of the color indication demonstrates the close identity between the two genomes since their last common ancestor, approximately 5 million years before present.

• The human chromosome 2 actually aligns to two separate chimp chromosomes, now called chr2a and chr2 and represented here by the same color..

• Data for this figure comes from assemblies of the human and chimpanzee genomes available from the UCSC Genome Browser in June 2006.

Benefits of comparative genomics Identifying DNA sequences that have been "conserved“It pinpoints genes that are essential to life and highlights genomic signals

that control gene function across many speciesComparative genomics also provides a powerful tool for studying evolution

Applications• agriculture,• biotechnology • and zoology• evolutionary tree• Drugs discovery

Comparative Genomics in Drug Discovery

Comparative genomic studies throw important light on the pathogenesis of organisms, throwing up opportunities for therapeutic intervention as well as help in understanding and identifying disease genes

One of the most important fallouts of comparative analyses at a genome-wide scale is in the ability to identify and develop novel drug targets

Comparative genomics in drug discovery programs. A flow chart diagram explaining how comparative genomics can facilitate drug discovery programs for

the discovery of new antimicrobials

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www.powershow.com/view1/1fa4ca-ZDc1Z/UCSC_Genome_Browser_Tutorial_powerpoint_ppt_presentation

6. http://www.dcode.org/7. http://blast.ncbi.nlm.nih.gov/Blast.cgi8. http://

www.proteinstructures.com/Sequence/Sequence/sequence-alignment.html9. https://www.dnalc.org/view/1241-Breakpoints.html