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Fig. 1 | Genome Biology

Fig. 1

From: Next-generation microbiology: from comparative genomics to gene function

Fig. 1

| Schematic overview of the GWAS and Tn-seq methods and a generalised validation pipeline. The gene highlighted in orange represents an idealised output for each approach. GWAS panels: In general, samples used for GWAS studies are directly isolated from the environment of interest. The phenotype of each isolate is tested and/or recorded, before whole-genome sequencing. Correlations between changes in observed genotypes and phenotype variations are determined. The output of GWAS can be displayed as a Manhattan plot, with the probability that each genetic variant detected in a population is associated with the phenotype of interest plotted against the genome positions. If variants fall above a certain probability threshold (dotted line), they are considered associated with the phenotype of interest (points highlighted in orange). Tn-seq panels: Saturated transposon libraries are grown in the presence and absence of the selection pressure of interest. Transposon-genome junctions from each member of the library are amplified and sequenced. Exploiting the quantitative function of massive parallel sequencing, the number of reads found for each transposon insertion junction are plotted against the genome position. The datasets obtained from libraries with and without the selection pressure are then compared to identify the contribution of each gene to the fitness. Areas of the genome with a different pattern of transposon insertions are deemed to be associated with the selection conditions (see region within the orange box). Validation panels: Initially the results of both methods are validated statistically and first insights into gene function are gained through literature and database searches. Deeper studies confirm the genotype-phenotype relationship of the results with a functional validation in the laboratory using a variety of experimental approaches

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