MycoBASE: expanding the functional annotation coverage of mycobacterial genomes

Abstract

Background: Central to most omic scale experiments is the interpretation and examination of resulting gene lists corresponding to differentially expressed, regulated, or observed gene or protein sets. Complicating interpretation is a lack of functional annotation assigned to a large percentage of many microbial genomes. This is particularly noticeable in mycobacterial genomes, which are significantly divergent from many of the microbial model species used for gene and protein functional characterization, but which are extremely important clinically. Mycobacterial species, ranging from M. tuberculosis to M. abscessus, are responsible for deadly infectious diseases that kill over 1.5 million people each year across the world. A better understanding of the coding capacity of mycobacterial genomes is therefore necessary to shed increasing light on putative mechanisms of virulence, pathogenesis, and functional adaptations.

Description: Here we describe the improved functional annotation coverage of 11 important mycobacterial genomes, many involved in human diseases including tuberculosis, leprosy, and nontuberculous mycobacterial (NTM) infections. Of the 11 mycobacterial genomes, we provide 9899 new functional annotations, compared to NCBI and TBDB annotations, for genes previously characterized as genes of unknown function, hypothetical, and hypothetical conserved proteins. Functional annotations are available at our newly developed web resource MycoBASE (Mycobacterial Annotation Server) at strong.ucdenver.edu/mycobase.

Conclusion: Improved annotations allow for better understanding and interpretation of genomic and transcriptomic experiments, including analyzing the functional implications of insertions, deletions, and mutations, inferring the function of understudied genes, and determining functional changes resulting from differential expression studies. MycoBASE provides a valuable resource for mycobacterial researchers, through improved and searchable functional annotations and functional enrichment strategies. MycoBASE will be continually supported and updated to include new genomes, enabling a powerful resource to aid the quest to better understand these important pathogenic and environmental species.

Fig. 1

Pipeline for creating improved annotations. Input files were taken from NCBI and TBDB and then annotated using Blannotator and PHAST. The resulting annotations were then used to create databases containing GO terms and a collection of functional, phage, and transposon annotations

Fig. 2

Annotation improvement in the 11 mycobacterial genomes. a Proportion of genes with original functional annotations (black), GO term annotations (green), and improved functional annotations (blue). b Proportion of original functional annotations with a corresponding improved functional annotation (black), and the proportion of these annotations that are more significantly similar than background (red)

Fig. 3

Database structure. Database containing two tables. The first table contains gene features for a given genome. The second table contains GO terms for all genes. These two tables are linked together by gene IDs

Fig. 4

Extracting annotations by gene name from website. To download annotations by gene name first click on the “Annotation” link on the website. Next select your genome of interest from the species dropdown menu. Select the “Search gene names” option button then insert a list of gene names separated by a comma or newline character. Next hit the “Submit” button and the list of annotations associated with the gene names will be downloaded

Fig. 5

Insertion of gene cassette in Mycobacterium abscessus strain ATCC 19977. Insertion of a 37KB insertion region encoding for a cassette of eight biphenyl and aromatic hydrocarbon degradation enzymes (red arrows). Conserved genes within MAB and MBOL are shown in green, and 34 inserted genes are shown in blue and red

Fig. 6

Gene ontology 1 taxa terms. Proportion of the 545 GO terms that are unique to one genome. MSMEG contains the majority of 1 taxa terms, owing to its larger genome and diversity of chemicals that it can metabolize and synthesize

Fig. 7

Ratio of genes in enriched GO terms. Plot of the 10 genome pairs with more than one enriched gene. The ratio is the number of genes with a given GO term in one genome over the number of genes with that same GO term in the other genome