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08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies
Nicola Segata1, Curtis Huttenhower
1Biostatistics Department, Harvard School of Public Health, Harvard University, Boston, Massachusetts, United States of America.
Plos One
|September 21, 2011
Summary
Researchers identified conserved core genes in microbes using high-throughput sequencing. These genes improve microbial community analysis and phylogenetic studies, complementing traditional marker genes like 16S rDNA.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- High-throughput sequencing enables analysis of microbial community metagenomes and genomes.
- Taxonomic marker genes (e.g., 16S rDNA) are used for community assessment and phylogeny reconstruction.
- There is a need for conserved core genes as effective taxonomic markers and for functional characterization.
Purpose of the Study:
- To develop a method for bioinformatically identifying ubiquitous core genes in microbial clades.
- To assess the utility of these core genes for comparative genomics and microbial community structure determination.
- To characterize the biological functions enriched within conserved core genes.
Main Methods:
- A recursive method was employed to identify core genes from a large dataset of complete microbial genomes (>1,100).
- Core gene sets were generated for 2,861 bacterial and archaeal clades.
- Phylogenetic trees were constructed using identified core genes and compared with 16S rDNA-based phylogenies.
Main Results:
- Core gene set sizes inversely correlated with clade alpha-diversity.
- Identified core genes are enriched in essential functions like translation, transcription, replication, and regulation.
- Phylogenies derived from core genes showed agreement with 16S rDNA-based phylogenies.
- Functional phylogenies based on gene presence/absence complemented sequence-based phylogenies.
Conclusions:
- Systematic selection of core genes can optimize comparative genomics and microbial community structure analysis.
- Conserved core genes provide reliable phylogenetic markers and insights into conserved biological functions.
- This approach offers a valuable complement to traditional molecular phylogenetics.
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