Phylogenomics is a field that deals with the analysis of family trees using sequenced genomes . The methods of phylogenetics are applied to genomes, partly also to DNA generated from transcriptomes by reverse transcription .
Phylogenomics is used to predict the function of an unknown protein on the basis of similar proteins with known functions by comparing the DNA sequences . Furthermore, she investigates lineages and relationships, the occurrence of horizontal gene transfers and the evolutionary development of gene families and the resulting protein families within a species .
The analysis is carried out using bioinformatic methods because of the comparatively large data sets to be compared . The analysis of many genes improves the test strength . The methods can be divided into five groups, based on different genes, based on the content of the gene, based on the arrangement of genes, K-string based and based on metabolic pathways . While most methods are based on an assignment of homologous sequence sections ( sequence alignment ), which becomes more and more complex with increasing length and with decreasing relationship of the sequences and ultimately becomes impossible for the comparison of entire genomes, the K-string method is assignment-free; Later on, a number of other methods without alignment were developed, some of which require less computing power. Depending on the selected calculation method, different family trees can occasionally be created from the same data set.
In the analyzes, there are various basic assumptions such as the preservation of sequences over time, the equivalence of the methods in pedigrees and the evolution of gene or protein families, simple nucleated cells as the origin of all life and the horizontal gene transfer as the cause of incongruities in various analyzes Genes (including the formation of endosymbionts ).
Phylogenomic methods are e.g. B. the genome sequencing , the sequencing of the rDNA , the multilocus sequence typing and the multilocus sequence analysis . Evolutionary lineages are recorded in the PhylomeDB database .
The term phylogenomics was coined in 1997 by Jonathan Eisen and originally only included the prediction of the function of a protein based on the similarities of DNA sequences. In 1998 he worked out the methodology for this. The formation of protein families was described by Emile Zuckerkandl and Linus Pauling in 1965 , about 35 years before the first sequenced genomes. The use of genomes to create evolutionary pedigrees as part of phylogenomics began in the early 2000s and was first fully described in 2005.
- Rob DeSalle: Phylogenomics. Garland Science, 2012, ISBN 978-1-135-03871-7 .
- William J. Murphy: Phylogenomics. Humana Press, 2008, ISBN 978-1-58829-764-8 .
- Marco Fondi: Bioinformatics of Genome Evolution: from Ancestral to Modern Metabolism Phylogenomics and Comparative Genomics to Understand Microbial Evolution. Firenze University Press, 2011, ISBN 978-88-6655-043-3 .
- A. Som: Causes, consequences and solutions of phylogenetic incongruence. In: Briefings in bioinformatics. Volume 16, Number 3, May 2015, pp. 536-548, doi: 10.1093 / bib / bbu015 . PMID 24872401 .
- E. Pennisi: Evolution. Building the tree of life, genome by genome. In: Science. Volume 320, Number 5884, June 2008, pp. 1716–1717, doi: 10.1126 / science.320.5884.1716 . PMID 18583591 .
- JT Cannon, KM Kocot: Phylogenomics Using Transcriptome Data. In: Methods in molecular biology (Clifton, NJ). Volume 1452, 2016, pp. 65-80, doi : 10.1007 / 978-1-4939-3774-5_4 . PMID 27460370 .
- JW Whitaker, GA McConkey, DR Westhead: The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. In: Genome biology. Volume 10, number 4, 2009, p. R36, doi: 10.1186 / gb-2009-10-4-r36 . PMID 19368726 , PMC 2688927 (free full text).
- Q. Ong, P. Nguyen, NP Thao, L. Le: Bioinformatics Approach in Plant Genomic Research. In: Current genomics. Volume 17, Number 4, August 2016, pp. 368-378, doi: 10.2174 / 1389202917666160331202956 . PMID 27499685 , PMC 4955030 (free full text).
- S. Kumar, AJ Filipski, FU Battistuzzi, SL Kosakovsky Pond, K. Tamura: Statistics and truth in phylogenomics. In: Molecular biology and evolution. Volume 29, Number 2, February 2012, pp. 457-472, doi: 10.1093 / molbev / msr202 . PMID 21873298 , PMC 3258035 (free full text).
- Z. Wang, Z. Xie, Y. Cai, K. Shu, F. Huang: Advances in phylogenomics. In: Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji. Volume 36, Number 7, July 2014, pp. 669-678, doi: 10.3724 / SP.J.1005.2014.0669 . PMID 25076031 .
- Hervé Philippe, Frederic Delsuc, Henner Brinkmann, Nicolas Lartillot: Phylogenomics. In: Annual Review of Ecology, Evolution, and Systematics. Volume 36, 2005, pp. 541-562. doi: 10.1146 / annurev.ecolsys.35.112202.130205 .
- CG Kurland, A. Harish: The phylogenomics of protein structures: The backstory. In: Biochemistry. Volume 119, December 2015, pp. 284-302, doi: 10.1016 / j.biochi.2015.07.027 . PMID 26234735 .
- B. Boussau, V. Daubin: Genomes as documents of evolutionary history. In: Trends in ecology & evolution. Volume 25, Number 4, April 2010, pp. 224-232, doi: 10.1016 / j.tree.2009.09.007 . PMID 19880211
- MJ Seufferheld, G. Caetano-Anollés: Phylogenomics supports a cellularly structured urancestor. In: Journal of molecular microbiology and biotechnology. Volume 23, number 1–2, 2013, pp. 178–191, doi: 10.1159 / 000346552 . PMID 23615204 .
- F. Burki, K. Shalchian-Tabrizi, J. Pawlowski: Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. In: Biology letters. Volume 4, number 4, August 2008, pp. 366-369, doi: 10.1098 / rsbl.2008.0224 . PMID 18522922 , PMC 2610160 (free full text).
- J. Huerta-Cepas, S. Capella-Gutiérrez, LP Pryszcz, M. Marcet-Houben, T. Gabaldón: PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. In: Nucleic acids research. Volume 42, Database issue January 2014, pp. D897 – D902, doi: 10.1093 / nar / gkt1177 . PMID 24275491 , PMC 3964985 (free full text).
- JA Eisen, D. Kaiser, RM Myers: Gastrogenomic delights: a movable feast. In: Nature medicine. Volume 3, Number 10, October 1997, pp. 1076-1078. PMID 9334711 , PMC 3155951 (free full text).
- JA Eisen: Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. In: Genome research. Volume 8, Number 3, March 1998, pp. 163-167. PMID 9521918 .
- E. Zuckerkandl, L. Pauling: Evolutionary divergence and convergence in proteins. In: V. Bryson, HJ Vogel: Evolving genes and proteins . Academic Press, New York 1965, pp. 97-166.
- Jonathan A. Eisen, Claire M. Fraser: Phylogenomics: Intersection of Evolution and Genomics. In: Science. 300, 2003, pp. 1706-1707.
- F. Delsuc, H. Brinkmann, H. Philippe: Phylogenomics and the reconstruction of the tree of life. In: Nature Reviews Genetics . Volume 6, number 5, May 2005, pp. 361-375, doi: 10.1038 / nrg1603 . PMID 15861208 .