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Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
- Source :
- Briefings in Bioinformatics, Briefings in Bioinformatics, 22(3), 1. Oxford University Press
- Publication Year :
- 2020
- Publisher :
- Oxford University Press, 2020.
-
Abstract
- Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins. This manual analysis limits the possibility of including more protein-complex components, repeating the analyses for updated genome sets or expanding the analyses to larger scales. Automated orthology inference should allow such large-scale analyses, but substantial differences between orthologous groups generated by different approaches are observed. We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regard to genome evolution in eukaryotes. Specifically, we investigate phylogenetic profile similarity (co-occurrence of complexes), the last eukaryotic common ancestor’s gene content, pervasiveness of gene loss and the overlap with manually determined orthologous groups. Moreover, we compare the inferred orthologies to each other. We find that most orthology methods reconstruct a large last eukaryotic common ancestor, with substantial gene loss, and can predict interacting proteins reasonably well when applying phylogenetic co-occurrence. At the same time, derived orthologous groups show imperfect overlap with manually curated orthologous groups. There is no strong indication of which orthology method performs better than another on individual or all of these aspects. Counterintuitively, despite the orthology methods behaving similarly regarding large-scale evaluation, the obtained orthologous groups differ vastly from one another. Availability and implementation The data and code underlying this article are available in github and/or upon reasonable request to the corresponding author: https://github.com/ESDeutekom/ComparingOrthologies.
- Subjects :
- Genome evolution
AcademicSubjects/SCI01060
Proteome
Inference
Computational biology
Biology
Genome
Evolution, Molecular
03 medical and health sciences
0302 clinical medicine
eukaryotes
Similarity (network science)
co-occurrence
Databases, Protein
Gene
Molecular Biology
Phylogeny
030304 developmental biology
Method Review
0303 health sciences
Internet
Phylogenetic tree
Co-occurrence
Eukaryota
Proteins
Reproducibility of Results
gene loss
Genomics
orthology inference
Benchmarking
Phylogenetic Pattern
030217 neurology & neurosurgery
Software
Information Systems
orthologous groups
Subjects
Details
- Language :
- English
- ISSN :
- 14774054 and 14675463
- Volume :
- 22
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- Briefings in Bioinformatics
- Accession number :
- edsair.doi.dedup.....eae49bf75f6e36c7bb5341a0246eea47