Download Phylogenomics www.AssignmentPoint.com Phylogenomics is the

Phylogenomics
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Phylogenomics is the intersection of the fields of evolution and genomics. The
term has been used in multiple ways to refer to analysis that involves genome
data and evolutionary reconstructions. It is a group of techniques within the
larger fields of phylogenetics and genomics. Phylogenomics draws information
by comparing entire genomes, or at least large portions of genomes.
Phylogenetics compares and analyzes the sequences of single genes, or a small
number of genes, as well as many other types of data. Four major areas fall
under phylogenomics:
 Prediction of gene function
 Establishment and clarification of evolutionary relationships
 Gene family evolution
 Prediction and retracing lateral gene transfer.
Prediction of Gene Function
When Jonathan Eisen originally coined phylogenomics, it applied to prediction
of gene function. Before the use of phylogenomic techniques, predicting gene
function was done primarily by comparing the gene sequence with the
sequences of genes with known functions. When several genes with similar
sequences but differing functions are involved, this method alone is ineffective
in determining function. A specific example is presented in the paper
“Gastronomic Delights: A movable feast”. Gene predictions based on sequence
similarity alone had been used to predict that Helicobacter pylori can repair
mismatched DNA. This prediction was based on the fact that this organism has
a gene for which the sequence is highly similar to genes from other species in
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the "MutS" gene family which included many known to be involved in
mismatch repair. However, Eisen noted that H. pylori lacks other genes thought
to be essential for this function (specifically, members of the MutL family).
Eisen suggested a solution to this apparent discrepancy - phylogenetic trees of
genes in the MutS family revealed that the gene found in H. pylori was not in
the same subfamily as those known to be involved in mismatch repair.
Furthermore, he suggested that this "phylogenomic" approach could be used as
a general method for prediction functions of genes. This approach was formally
described in 1998. For reviews of this aspect of phylogenomics see Brown D,
Sjölander K. Functional classification using phylogenomic inference.
Prediction and Retracing Lateral Gene Transfer
Traditional phylogenetic techniques have difficulty establishing differences
between genes that are similar because of lateral gene transfer and those that are
similar because the organisms shared an ancestor. By comparing large numbers
of genes or entire genomes among many species, it is possible to identify
transferred genes, since these sequences behave differently from what is
expected given the taxonomy of the organism. Using these methods, researchers
were able to identify over 2,000 metabolic enzymes obtained by various
eukaryotic parasites from lateral gene transfer.
Gene family evolution
The comparison of complete gene sets for a group of organisms allow the
identification of events in gene evolution such as gene duplication or gene
deletion. The evolutionary relevance of this events is really big. For example,
multiple duplications of genes encoding degradative enzymes of certain families
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is a common adaptation in microbes to new nutrient sources. On the contrary,
loss of genes is important in reductive evolution, such as in intracellular
parasites or symbionts. Whole genome duplication events, which potentially
duplicate all the genes in a genome at once, are drastic evolutive events with
great relevance in the evolution of many clades, and whose signal can be traced
with phylogenomic methods.
Establishment of Evolutionary Relationships
Traditional single-gene studies are effective in establishing phylogenetic trees
among closely related organisms, but have drawbacks when comparing more
distantly related organisms or microorganisms. This is because of lateral gene
transfer, convergence, and varying rates of evolution for different genes. By
using entire genomes in these comparisons, the anomalies created from these
factors are overwhelmed by the pattern of evolution indicated by the majority of
the data. Through phylogenomics, it has been discovered that most of the
photosynthetic eukaryotes are linked and possibly share a single ancestor.
Researchers compared 135 genes from 65 different species of photosynthetic
organisms. These included plants, chromalveolates, rhizarians, haptophytes and
cryptomonads. This has been referred to as the Plants+HC+SAR megagroup.
Using this method, it is theoretically possible to create fully resolved
phylogenetic trees, and timing constraints can be recovered more accurately.
However, in practice this is not always the case. Due to insufficient data,
multiple trees can sometimes be supported by the same data when analyzed
using different methods.
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