Phylogenomics

Phylogenomics is the intersection of the fields of evolution and genomics.[1] The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions.[2] 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.[3] 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.

The ultimate goal of phylogenomics is to reconstruct the evolutionary history of species through their genomes. This history is usually inferred from a series of genomes by using a genome evolution model and standard statistical inference methods (e.g. Bayesian inference or maximum likelihood estimation).[4]

## Contents

* 1 Prediction of gene function
* 2 Prediction and retracing lateral gene transfer
* 3 Gene family evolution
* 4 Establishment of evolutionary relationships
* 5 Databases
* 6 See also
* 7 References
* 8 Further reading

## 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".[5] Gene predictions based on sequence similarity alone had been used to predict that Helicobacter pylori can repair mismatched DNA.[6] 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 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.[5] 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.[7] For reviews of this aspect of phylogenomics see Brown D, Sjölander K. Functional classification using phylogenomic inference.[8][9]

## 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.[10]

## Gene family evolution

The comparison of complete gene sets for a group of organisms allows the identification of events in gene evolution such as gene duplication or gene deletion. Often, such events are evolutionarily relevant. For example, multiple duplications of genes encoding degradative enzymes of certain families 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 evolutionary 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.[11][12][13] Using this method, it is theoretically possible to create fully resolved phylogenetic trees, and timing constraints can be recovered more accurately.[14][15] 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.[16]

Notable results of phylogenomics (in the sense of massive multigene phylogenies):

* Using 135 genes from 65 different species of photosynthetic organisms, it has been discovered that most of the photosynthetic eukaryotes are linked and possibly share a single ancestor. These included plants, alveolates, rhizarians, haptophytes and cryptomonads. This has been referred to as the Plants+HC+SAR megagroup. This study concatenates these genes together in what's called a "supermatrix" approach.[17]
* The root of the bacterial tree of life and the extent of horizontal gene transfer was determined by tracing the evolution of 11,272 gene families. This is a "supertree" approach.[18]
* The root of the archaeal tree of life was determined using a 45-protein supermatrix analysis and a 3242-protein supertree analysis. The 31,236 gene families in archaea are then put on the tree to determine what the ancestral archaea may have.[19]
* Using 120 proteins from bacteria or 53 proteins from archaea (supermatrix), the Genome Taxonomy Database generates a taxonomy of all bacteria and archaea with high-quality sequenced genomes.[20]

Using massive multigene phylogenies to classify organisms does not necessarily require the use of whole genomes. A 2023 study uses target enrichment to selectively sequence the 114 chosen marker genes, reducing the cost of the work by skipping irrelevant sequences.[21]

## Databases

1. PhylomeDB

## See also

* Archaeopteryx (phylogenomics software)
* Microbial phylogenetics
* Phylogenetics
* Sequence alignment
* Supertree

## References

1. ↑ "Overview of the First Phylogenomics Conference". BMC Ecol. Evol. 7 (Suppl 1): S1-16. 2007-02-08. doi:10.1186/1471-2148-7-S1-S1. PMID 17288567. Bibcode: 2007BMCEE...7S...1P.
2. ↑ "Statistics and truth in phylogenomics". Molecular Biology and Evolution 29 (2): 457–472. February 2012. doi:10.1093/molbev/msr202. PMID 21873298.
3. ↑ "Evolution. Building the tree of life, genome by genome". Science 320 (5884): 1716–1717. June 2008. doi:10.1126/science.320.5884.1716. PMID 18583591.
4. ↑ "2.1 To What Extent Current Limits of Phylogenomics Can Be Overcome?". Phylogenetics in the Genomic Era. 2020. pp. 2.1.1–2.1.34. https://hal.inria.fr/PGE.
5. ↑ 5.0 5.1 "Gastrogenomic delights: a movable feast". Nature Medicine 3 (10): 1076–1078. October 1997. doi:10.1038/nm1097-1076. PMID 9334711.
6. ↑ "The complete genome sequence of the gastric pathogen Helicobacter pylori". Nature 388 (6642): 539–547. August 1997. doi:10.1038/41483. PMID 9252185. Bibcode: 1997Natur.388..539T.
7. ↑ "Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis". Genome Research 8 (3): 163–167. March 1998. doi:10.1101/gr.8.3.163. PMID 9521918.
8. ↑ "Functional classification using phylogenomic inference". PLOS Computational Biology 2 (6): e77. June 2006. doi:10.1371/journal.pcbi.0020077. PMID 16846248. Bibcode: 2006PLSCB...2...77B.
9. ↑ "Phylogenomic inference of protein molecular function: advances and challenges". Bioinformatics 20 (2): 170–179. January 2004. doi:10.1093/bioinformatics/bth021. PMID 14734307.
10. ↑ "The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes". Genome Biology 10 (4). 2009. doi:10.1186/gb-2009-10-4-r36. PMID 19368726.
11. ↑ "Phylogenomics and the reconstruction of the tree of life". Nature Reviews. Genetics 6 (5): 361–375. May 2005. doi:10.1038/nrg1603. PMID 15861208.
12. ↑ Philippe H, Snell EA, Bapteste E, Lopez P, Holland PW, Casane D "Phylogenomics of eukaryotes: impact of missing data on large alignments Mol Biol Evol 2004 Sep;21(9):1740-52. .
13. ↑ "Phylogenomics: the beginning of incongruence?". Trends in Genetics 22 (4): 225–231. April 2006. doi:10.1016/j.tig.2006.02.003. PMID 16490279. https://hal.archives-ouvertes.fr/halsde-00315496/file/Jeffroy-TrendsGenet06_HAL.pdf.
14. ↑ "Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny". Proceedings. Biological Sciences 279 (1742): 3491–3500. September 2012. doi:10.1098/rspb.2012.0683. PMID 22628470.
15. ↑ "Phylogenomics of strongylocentrotid sea urchins". BMC Evolutionary Biology 13 (1). April 2013. doi:10.1186/1471-2148-13-88. PMID 23617542. Bibcode: 2013BMCEE..13...88K.
16. ↑ Philippe, Herve'; Delsuc, Frederic; Brinkmann, Henner; Lartillot, Nicolas (2005). "Phylogenomics". Annual Review of Ecology, Evolution, and Systematics 36 (1): 541–562. doi:10.1146/annurev.ecolsys.35.112202.130205. Bibcode: 2005AREES..36..541P.
17. ↑ "Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes". Biology Letters 4 (4): 366–369. August 2008. doi:10.1098/rsbl.2008.0224. PMID 18522922.
18. ↑ Coleman, Gareth A.; Davín, Adrián A.; Mahendrarajah, Tara A.; Szánthó, Lénárd L.; Spang, Anja; Hugenholtz, Philip; Szöllősi, Gergely J.; Williams, Tom A. (7 May 2021). "A rooted phylogeny resolves early bacterial evolution". Science 372 (6542). doi:10.1126/science.abe0511. PMID 33958449. Bibcode: 2021Sci...372e0511C.
19. ↑ Williams, Tom A.; Szöllősi, Gergely J.; Spang, Anja; Foster, Peter G.; Heaps, Sarah E.; Boussau, Bastien; Ettema, Thijs J. G.; Embley, T. Martin (6 June 2017). "Integrative modeling of gene and genome evolution roots the archaeal tree of life". Proceedings of the National Academy of Sciences 114 (23): E4602–E4611. doi:10.1073/pnas.1618463114. PMID 28533395. Bibcode: 2017PNAS..114E4602W.
20. ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea.". Nature Biotechnology 38 (9): 1079–1086. doi:10.1038/s41587-020-0501-8. PMID 32341564. https://www.researchgate.net/publication/340954053.
21. ↑ Yu, PL; Fulton, JC; Hudson, OH; Huguet-Tapia, JC; Brawner, JT (2 October 2023). "Next-generation fungal identification using target enrichment and Nanopore sequencing.". BMC Genomics 24 (1): 581. doi:10.1186/s12864-023-09691-w. PMID 37784013.

## Further reading

* Williams, Tom A; Davin, Adrian A; Szánthó, Lénárd L; Stamatakis, Alexandros; Wahl, Noah A; Woodcroft, Ben J; Soo, Rochelle M; Eme, Laura et al. (8 January 2024). "Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution". The ISME Journal 18 (1). doi:10.1093/ismejo/wrae129. PMID 39001714.
* Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd; Rokas, Antonis (1 February 2018). "Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets". Molecular Biology and Evolution 35 (2): 486–503. doi:10.1093/molbev/msx302. PMID 29177474. (compares RAxML/ExaML, PhyML, IQ-TREE, and FastTree)

* v
* t
* e

Phylogenetics

Relevant fields|

* Computational phylogenetics
* Molecular phylogenetics
* Cladistics
* Taxonomy
* Evolutionary taxonomy
* Systematics

Note: This topic belongs to "Evolutionary biology" portal

Basic concepts|

* Phylogenesis
* Cladogenesis
* Phylogenetic tree
* Cladogram
* Phylogenetic network
* Long branch attraction
* Clade vs Grade
* Lineage
* Ghost lineage
* Ghost population

Inference methods|

* Maximum parsimony
* Probabilistic methods
* Maximum likelihood
* Bayesian inference
* Distance-matrix methods
* Neighbor-joining
* UPGMA
* Least squares
* Three-taxon analysis

Current topics|

* PhyloCode
* DNA barcoding
* Molecular phylogenetics
* Phylogenetic comparative methods
* Phylogenetic niche conservatism
* Phylogenetics software
* Phylogenomics
* Phylogeography

Group traits|

* Primitive
* Plesiomorphy
* Symplesiomorphy
* Derived
* Apomorphy
* Synapomorphy
* Autapomorphy

Group types|

* Monophyly
* Paraphyly
* Polyphyly

Nomenclature|

* Phylogenetic nomenclature
* Crown group
* Sister group
* Basal
* Supertree

* Category
* Commons

0.00

(0 votes)

Original source: https://en.wikipedia.org/wiki/Phylogenomics. Read more

|

Retrieved from "https://handwiki.org/wiki/index.php?title=Biology:Phylogenomics&oldid=4262571"
*[v]: View this template
*[t]: Discuss this template
*[e]: Edit this template