Abstract
There is an increasing availability of complete or draft genome sequences for microbial organisms. These data form a potentially valuable resource for genotype-phenotype association and gene function prediction, provided that phenotypes are consistently annotated for all the sequenced strains. In this review, we address the requirements for successful gene-trait matching. We outline a basic protocol for microbial functional genomics, including genome assembly, annotation of genotypes (including single nucleotide polymorphisms, orthologous groups and prophages), data pre-processing, genotype-phenotype association, visualization and interpretation of results. The methodologies for association described herein can be applied to other data types, opening up possibilities to analyze transcriptome-phenotype associations, and correlate microbial population structure or activity, as measured by metagenomics, to environmental parameters. © The Author 2013. Published by Oxford University Press.
| Original language | English |
|---|---|
| Article number | elt008 |
| Pages (from-to) | 366-380 |
| Number of pages | 15 |
| Journal | Briefings in Functional Genomics |
| Volume | 12 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - 1 Jul 2013 |
Keywords
- Functional genomics
- Genome-wide association studies
- Genotype-phenotype association
- Microbial genomics
- Random forest
- DNA fragment
- article
- Aspergillus fumigatus
- Bacilli
- DNA integration
- DNA replication
- DNA sequence
- eukaryotic cell
- functional genomics
- gain of function mutation
- gene function
- genetic association
- genomics
- genotype phenotype correlation
- Lactobacillales
- Lactococcus lactis
- loss of function mutation
- microbial genetics
- multigene family
- nonhuman
- nucleotide sequence
- open reading frame
- pathogenicity
- phenotype
- phylogenetic tree
- point mutation
- prophage
- random forest
- single nucleotide polymorphism
- Sinorhizobium meliloti
- stop codon