Phylogenomics
Encyclopedia
Phylogenomics can be regarded as the intersection between the fields of evolution
and genomics
. The term has been used in multiple ways to refer to some type of analysis involving genome
data and evolutionary reconstructions. It is an expansion of earlier phylogenetics
. Phylogenomics draws information from the comparison of entire genomes, or at least large groups of genes made of several megabases. Phylogenetics can be considered smaller in scope and concerns the comparison and analysis of only single genes or a very small number of genes. There are three major areas of focus that fall under the category of phylogenomics. These are the prediction of a gene function, establishment and clarification of evolutionary relationships, and predicting and retracing lateral gene transfer.
originally coined the term phylogenomics it was being applied to the prediction of gene function. Before the use of phylogenomic techniques, predicting gene function was done primarily through the comparison of the gene sequence with the sequences of genes with known function. 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 suggest that Helicobacter pylori has the ability the repair mismatched DNA
. This comes from the fact that this organism has genes with sequences very similar to two groups of genes found in E. coli which our known to be involved in mismatch repair. However, H. pylori lacks other genes essential for this function, suggesting these genes may have an alternative function. The solution suggested by J. Eisen was to construct a phylogenetic tree for the genes in question and then combine this information with the standard sequence similarity data. For reviews of this aspect of phylogenomics see Brown D, Sjölander K. Functional classification using phylogenomic inference.
, 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. 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.
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
and genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
. The term has been used in multiple ways to refer to some type of analysis involving genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
data and evolutionary reconstructions. It is an expansion of earlier phylogenetics
Phylogenetics
In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...
. Phylogenomics draws information from the comparison of entire genomes, or at least large groups of genes made of several megabases. Phylogenetics can be considered smaller in scope and concerns the comparison and analysis of only single genes or a very small number of genes. There are three major areas of focus that fall under the category of phylogenomics. These are the prediction of a gene function, establishment and clarification of evolutionary relationships, and predicting and retracing lateral gene transfer.
Prediction of Gene Function
When Jonathan EisenJonathan Eisen
Jonathan A. Eisen is an American evolutionary biologist, currently working at University of California, Davis. His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the academic editor-in-chief of the open-access journal PLoS Biology.In 2011 Eisen was...
originally coined the term phylogenomics it was being applied to the prediction of gene function. Before the use of phylogenomic techniques, predicting gene function was done primarily through the comparison of the gene sequence with the sequences of genes with known function. 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 suggest that Helicobacter pylori has the ability the repair mismatched DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
. This comes from the fact that this organism has genes with sequences very similar to two groups of genes found in E. coli which our known to be involved in mismatch repair. However, H. pylori lacks other genes essential for this function, suggesting these genes may have an alternative function. The solution suggested by J. Eisen was to construct a phylogenetic tree for the genes in question and then combine this information with the standard sequence similarity data. 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 difficulties in establishing the difference between genes which are similar because of lateral gene transfer and those which are similar because the organisms which possess it shared an ancestor. By comparing large numbers of genes or entire genomes among many species, the genes which were acquired through lateral gene transfer become more evident. Using these methods, researchers were able to identify over 2,000 metabolic enzymes obtained by various eukaryotic parasites from lateral gene transfer.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, convergenceConvergence
-Mathematics:* Convergence , refers to the notion that some functions and sequences approach a limit under certain conditions* Convergence , the notion that a sequence of transformations come to the same conclusion, no matter what order they are performed in.-Natural sciences:*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
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
of photosynthetic organisms. These included plants, chromalveolates, rhizarians, haptophytes and cryptomonads. This has been referred to as the Plants+HC+SAR megagroup
Plants+HC+SAR megagroup
Plants+HC+SAR megagroup is a group of eukaryotes.It includes:* Plants* Hacrobia * SAR supergroup...
.Using this method, it is theoretically possible to create fully resolved phylogenetic trees. 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.
See also
- Archaeopteryx
- Microbial phylogeneticsMicrobial phylogeneticsMicrobial phylogenetics is the study of the evolutionary relatedness among various groups of microorganisms. The molecular approach to microbial phylogenetic analysis, pioneered by Carl Woese in the 1970s and leading to the three-domain model , revolutionized our thinking about evolution in the...