4 Comparative Genomics

Comparative genomics is the study of the differences and similarities in genome structure and organization in
different organisms. There are two drivers for comparative genomics.
 One is a desire to have a much more detailed understanding of the process of evolution at the gross level (the
origin of the major classes of organism) and at a local level (what makes related species unique).
 The second driver is the need to translate DNA sequence data into proteins of known function.
The rationale here is that DNA sequences encoding important cellular functions are more likely to be conserved
between species than sequences encoding dispensable functions or non-coding sequences.

ORTHOLOGS AND PARALOGS

To compare genomes A and B in a meaningful manner, it is useful to determine which gene b in genome B
corresponds to gene a in genome A. This correspondence relationship is primarily based on homology. Functional
homology without sequence resemblance indicates evolutionary convergence (genes with no ancestral link but
identical function.) Sequence homology leads to a diagnosis of evolutionary divergence, starting from a common
ancestral sequence. In the frequent case of evolutionary divergence, the genes evolved from a common ancestor,
but diverged after speciation or following a duplication event
 When the homology is the result of speciation, such as when the history of the gene reflects that of the species
(for example, human and mouse alpha-hemoglobins), the genes are called orthologs (ortho =
‘correct’).Orthologues are homologous genes in different organisms that encode proteins with the same
function and which have evolved by direct vertical descent. They evolve simply by the gradual accumulation
of mutations.
 When the homology is the result of gene duplication, in which the two copies are transmitted side-by-side over
the history of a species (for example, mouse alpha- and beta-hemoglobin), the genes are known as paralogs,
(para = ‘in parallel’).Paralogues are homologous genes within an organism encoding proteins with related but
non-identical functions. They arise by gene duplication followed by mutation accumulation.
Ideally, one would expect orthologous genes in the genomes of two species to have the highest similarity,
considering their relatively recent divergence. The most direct approach to identifying orthologous genes therefore
consists in comparing all the genes in the two genomes with each other. The pairs of genes (a, b) that have the
most similarity are selected and considered orthologs.

The Clusters of Orthologous Groups (COGs) database has been designed to simplify evolutionary studies of
complete genomes and improve functional assignments of individual proteins. It consists of more than 2,800
conserved families of proteins (COGs) from each of the completely sequenced genomes. Each COG contains
orthologous sets of proteins from at least three phylogenetic lineages, which are assumed to have evolved from an
individual ancestral protein.

METABOLOMICS
Previously metabolism was defined as intracellular chemical reactions that produce chemical substances and
energies sustaining life. Through post-genome scientific studies, we have become aware of that life is based on
both chemical substances and genomic information. This adds a novel definition to metabolism; metabolism is
defined as the system where chemical substances and genomic information interact with each other in the network
of chemical reactions.
Metabolomics is defined as the measurement of the amounts (concentrations) and locations of the all the
metabolites in a cell, the metabolites being the small molecules transformed in the process of metabolism (i.e.,
mostly the substrates and products of enzymes).
The quantification of the amounts of expressed enzymes is proteomics; metabolomics is essentially an extension
of proteomics to the activities of the expressed enzymes, and it is of major interest to examine correlations between
expression data and metabolite data.
Metabolism and Metabolic Pathways
Metabolic pathway networks are also composed of links that are defined as a transformation of chemical structures
between two metabolites and an enzyme reaction. Metabolites and chemical mechanisms are the same throughout
biological species. Metabolism features the following two properties:
Multiplicity in metabolic pathway network
The metabolic pathway network contains the following three types of multiplicities
 Multiple links: When a metabolite is located on a branching point of a metabolic pathway, it has three or more
links. Any metabolic intermediate has at least two links as a product of the preceding enzyme reaction and as
a substrate of the following reaction.
 Isozymes: Two or more paralogous enzymes often catalyze the same transformation.
 Bypasses: Two metabolites are multiply linked through two or more metabolic pathways
Robustness of metabolite profile
The second property of metabolism is robustness of metabolite profile. Because every living organism possesses
its species-specific metabolic pathway network, the predetermined metabolite profiles also might be different from
species to species. Each phenotype in plants possesses a distinctive metabolite profile.
The bacterial cells regulate their metabolism to make the metabolite profile match the template under variable
environmental conditions. This is an example of the robustness of the metabolite profile.

Metabolome
The metabolome refers to the complete set of small-molecule chemicals found within a biological sample.[1] The
biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a bio fluid or an entire
organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites
that are naturally produced by an organism (such as amino acids, organic acids, nucleic acids, fatty acids, amines,
sugars, vitamins, co-factors, pigments, antibiotics, etc.) as well as exogenous chemicals (such as drugs,
environmental contaminants, food additives, toxins and other xenobiotics) that are not naturally produced by an
organism.

Metabolomic Analysis
Because metabolomics encompasses such an extensive network of biochemical interactions, many of which have
not yet been fully characterized in terms of participating reactants, different approaches to metabolome analyses
have arisen. Depending on the goal of one’s experiment, the approach used will differ.
The three principal approaches for the analysis of the metabolome are
 Metabolite profiling
Metabolite profiling is an approach that aims to identify and quantify metabolites, but does so on a biased scale
due to methodological limitations and differences in analytical platforms. Much of the bias in this technique is
introduced when extracting the sample from the organism or tissue of interest, and is due to differential
affinities for extraction solvents. Despite the introduced bias, this technique is, at present, the closest one can
get to a true and complete visualization of the metabolome
 Metabolic fingerprinting
Another approach in metabolomic technology is metabolic fingerprinting. This high-throughput approach is
normally utilized in tissue comparison or discrimination analysis, and so is simpler and coarser in its technique
(sample preparation, separation, and detection) in comparison to metabolic profiling.
 Metabonomics
Metabonomics is yet another aspect of metabolomics, which focuses on the metabolic response of organisms
to pathophysiological stimuli or genetic modification. This approach is generally restricted to microbiological
and other non-botanical studies.
Metabonomics is a subset of metabolomics and is defined as the quantitative measurement of the multi-
parametric metabolic responses of living systems to pathophysiological stimuli or genetic modification, with
particular emphasis on the elucidation of differences in population groups due to genetic modification, disease,
and environmental (including nutritional) stress.
Workflow of Metabolomics

Sample Collection from Sources

Sample Preparation
•HPLC/Column
•GC-MS
Extraction of Metabolites •Capillary Electrophoresis

•MS / SIMS
•NMR
Detection of Metabolites

Data Acquisition

Data Analysis using

Statistical Methods