MabsBase: a Mycobacterium abscessus genome and annotation database

Abstract

Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M. abscessus strains as well as resources for whole-genome annotations and computational predictions, to support the expanding scientific community interested in M. abscessus research. The MabsBase is freely available at http://mabscessus.um.edu.my.

Figure 1. Overview of MabsBase.

(A) The database overview which displays the main list of all strains and information such as genome size, genome identity and coverage etc., organized in columns. (B) ORF list of a specific strain. (C) Detailed information of an ORF with visualization in JBrowse.

Figure 2. A diagram showing the overview of the functionalities in MabsBase.

Figure 3. Core genome SNPs-based phylogenetic tree.

All isolates were clustered into three distinct groups. Countries where the sample collection originated are indicated in parentheses. Concatenated core genome SNPs sequences were aligned and phylogenetic inferences obtained using the maximum-likelihood method within the MEGA 5.1 software. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 1,000 times to generate a majority consensus tree. The scale bar represents a 6% sequence difference.