GenoVi, an open-source automated circular genome visualizer for bacteria and archaea
Source: GenoVi, an open-source automated circular genome visualizer for bacteria and archaea
Cumsille, Andrés, et al. “GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.” PLOS Computational Biology 19.4 (2023): e1010998.
OVERVIEW
The study introduces GenoVi, a Python command-line tool for creating custom circular genome representations and analyzing microbial genomes. It supports complete or draft genomes, offers customizable options including color palettes and text formatting, and integrates COG analysis. GenoVi automatically scales visualizations and generates COG histograms, heatmaps, and output tables. The tool was tested on Bacteria and Archaea genomes, including multipartite genomes. GenoVi is user-friendly, suitable for scientific publications, education, and outreach, and can be downloaded from https://github.com/robotoD/GenoVi.
BACKGROUND
The growth of genomic data has led to the availability of over 250,000 bacterial and archaeal genomes in public databases. Genomics and environmental genomics are being used in various fields to gain new knowledge and understand complex questions. Metagenome-assembled genomes (MAGs) are increasing due to metagenomic studies, creating a need for automated and user-friendly tools to analyze and interpret genomic information.
Circular genome visualization is a common method for analyzing and representing genomic elements. It involves displaying features such as GC content, GC skew, protein classification, and the location of tRNAs and rRNAs in a circular format. Several tools are available for circular genome visualization, but they often require complete chromosomes or plasmids and programming skills for complex customization. This limits their usability and hinders the implementation of complementary analyses.
In summary, the growing amount of genomic data necessitates the development of accessible and comprehensive tools for analyzing and visualizing genomes in a circular format, overcoming the limitations of existing tools.
RESULTS + DISCUSSION
GenoVi is a Python command-line tool that creates custom circular genome representations for microbial genomes. It takes a Genbank format file as input and performs various analyses and visualizations. It converts the file into a nucleotide fasta format and calculates GC content and GC skew. It also extracts information about CDS, tRNA, and rRNA. GenoVi predicts and classifies CDS into COG categories using the COG 2020 database through DeepNOG. It generates configuration files for Circos to create circular representations and provides output files such as COG histograms, COG frequency heatmaps, and tables of COG classification and general features. GenoVi is installed using a Conda environment and requires dependencies like NumPy, Pandas, Biopython, Matplotlib, and CairoSVG. It supports both draft and complete genomes and can be used with Genbank files from different annotators. The tool offers customizable options for colors, fonts, and background, and provides various scaling options. It outputs PNG and SVG files that can be further edited in vector editing programs. GenoVi is suitable for single genome representation and comparative genomic studies.
GenoVi is a tool that can be used for visualizing and analyzing genomic data, including draft genomes, complete genomes, and multiple genomes. It provides features for single and comparative genomics. For draft genomes, GenoVi creates a circular plot that includes each scaffold or contig in the same map. It can display information such as assembly length, GC content, and functional categories based on COG (Clusters of Orthologous Groups) analysis.
For complete genomes, GenoVi creates circular maps for each replicon (e.g., chromosome, plasmids) and scales the representation based on their length. It can also analyze GC skew to identify the origin and terminus of replication. GenoVi offers various options for COG representation, allowing the display of specific functional categories within a genome. This can be useful for genome mining of biosynthetic gene clusters or identifying genes of interest, such as non-ribosomal peptide synthetases (NRPSs).
In comparative genomics, GenoVi can analyze multiple genomes independently and generate output tables summarizing genomic features and COG information for each genome. These tables can facilitate comparative analysis and identification of genomic traits.
A case study using GenoVi on Paraburkholderia genomes demonstrated its potential for replicon classification. COG percentage distribution analysis revealed three major groups: chromosomes, chromids and megaplasmids, and plasmids. The functional patterns identified by GenoVi helped distinguish between different replicon types and provided insights into the genomic organization of Paraburkholderia.
Overall, GenoVi is a versatile tool for genome visualization and analysis, offering features for single genome analysis, comparative genomics, and identification of genomic traits.
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