Table 1.
Comparison of circular genome visualization software.
Fig 1.
(A) GenoVi incorporates several customizable options for visualization, such as an option for complete or draft genomes, twenty-five prebuilt color palettes, title, scale-up options, and COG categories selection. (B) GenoVi uses Genbank format files (gbff) as input. From each file GenoVi extracts CDS and RNAs position. Additionally, GenoVi converts this file into a nucleotide FASTA to calculate GC content, GC skew, and, if user-specified, into a protein FASTA to classify into COGs categories. (C) After calculating and formatting each genomic feature, GenoVi uses Circos to build a genome representation in svg and png format. COG abundance histogram, COG frequency heatmaps and summarizing tables of overall genomic features are also created in this step.
Fig 2.
Application of GenoVi using a draft or complete bacterial genome.
(A) GenoVi circular map of the draft genome of Corynebacterium alimapuense VA37-3T [18] (-s draft -cs paradise). Each contig is represented as separated bands of one circular representation. (B) GenoVi circular representation of the complete genome of Acinetobacter radioresistens DD78 [21] (-s complete, -cs autumn). Each circular map represents a replicon from the complete genome. A. radioresistens DD78 genome consists of a circular chromosome and three circular plasmids displayed next to the chromosome (—scale variable). Labeling from outside to the inside: Contigs; COGs on the forward strand; CDS, tRNAs, and rRNAs on the forward strand; CDS, tRNAs, and rRNAs on the reverse strand; COGs on the reverse strand; GC content; GC skew.
Fig 3.
High density of Translation, ribosomal structure and biogenesis (J) orthologs is located in the region 400–500 kb of Sulfolobus acidocaldarius DG1 genome.
(A) Genovi representation of the complete genome of S. acidocaldarius DG1 is depicted using default parameters (-s complete -cs paradise). (B) Most abundant five COG categories within the 400–550 kb range of DG1 genome are represented (—cogs 5), which included C (Energy production and conversion), E (Amino acid transport and metabolism), J (Translation, ribosomal structure, and biogenesis), K (Transcription) and R (General function prediction only). (C) Genovi representation of J category orthologs within the 400–550 kb genome of S. acidocaldarius DG1 (—cogs J).
Fig 4.
Visualization of NRPS biosynthetic gene clusters within the genome of Rhodococcus sp. H-CA8f.
Genovi representation of Rhodococcus sp. H-CA8f complete genome is depicted with an interior break in the ideogram to easily identify each track (-s complete, -cs dawn,—cogs Q, -te). Selection of Q orthologs (Secondary metabolites biosynthesis, transport, and metabolism) within the H-CA8f genome includes NPRS CDSs and can be easily seen by the whole genome representation.
Fig 5.
COG percentage distribution of Paraburkholderia replicons elucidates general functional patterns useful for its classification.
(A) COG percentage distribution of the 146 replicons from the Paraburkholderia genus. Hierarchical clustering revealed three distinct groups: Major chromosomes C1 (red); Minor chromosomes C2-C3-C4-C5-p1 (green); Plasmids (blue). CP&S: Cellular Processes and Signaling; IS&P: Information Storage and Processing; PC: Poorly Characterized. (B). Genomic features (size, GC-content, tRNA, and rRNA) from each replicon type were identified by COG percentage distribution. tRNA is the best feature to identify chromosomes (C1).
Fig 6.
Paraburkholderia terrae KU-15 visualization and analysis by GenoVi allows its replicon classification.
(A) Complete genome representation of P. terrae KU-15 using the blossom palette (-cs blossom). (B) Heatmap generated by GenoVi representing COG percentage frequency of each replicon of P. terrae KU-15 genome. Red boxes highlight key COG categories to differentiate each replicon type.