EDGAR 2.0: an enhanced software platform for comparative gene content analyses

Abstract

The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on the comparison of closely related genomes. By utilizing comparative approaches on gene level it is possible to gain insights into the core genes which represent the set of shared features for a set of organisms under study. Vice versa singleton genes can be identified to elucidate the specific properties of an individual genome. Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics. Over the last years, the software has been continuously improved and a large number of new analysis features have been added. For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented. Among other new features, EDGAR 2.0 provides extended phylogenetic analysis features like AAI (Average Amino Acid Identity) and ANI (Average Nucleotide Identity) matrices, genome set size statistics and modernized visualizations like interactive synteny plots or Venn diagrams. Thereby, the software supports a quick and user-friendly survey of evolutionary relationships between microbial genomes and simplifies the process of obtaining new biological insights into their differential gene content. All features are offered to the scientific community via a web-based and therefore platform-independent user interface, which allows easy browsing of precomputed datasets. The web server is accessible at http://edgar.computational.bio.

Figure 1.

Synteny plot of four Xanthomonas campestris chromosomes compared to X. campestris pv. campestris strain B100.

Figure 2.

(A) Core genome development plot for 14 Xanthomonas genomes. The red curve shows the fitted exponential decay function, blue and green curves indicate the upper and lower boundary of the 95% confidence interval. The extrapolated core genome size is 2364 genes. (B) Pan genome development plot for 14 Xanthomonas genomes. The red curve shows the fitted exponential Heaps’ law function, blue and green curves indicate the upper and lower boundary of the 95% confidence interval. Based on these results the pan genome is considered to be open with a growth exponent of 0.409.

Figure 3.

Pan versus core development plot of 15 Xanthomonas campestris genomes. The drastic drop of the core genome size with the introduction of Xanthomonas albilineans strain GPE PC73 is clearly visible. The outlier status of this genome is confirmed by the phylogenetic tree.