Development of ListeriaBase and comparative analysis of Listeria monocytogenes. (December 2015)

• Record Type: Journal Article
• Authors: Tan, Mui; Siow, Cheuk; Dutta, Avirup; Mutha, Naresh; Wee, Wei; Heydari, Hamed; Tan, Shi; Ang, Mia; Wong, Guat; Choo, Siew
• Is Part Of: BMC genomics. Volume 16:Number 1(2015)
• Page Start: 1
• Page End: 19
• Publication Date: 2015-12
• Subjects: ListeriaBase -- Listeria -- Comparative analysis; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-015-1959-5
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. WithListeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny ofListeria spp., leading to better management of the diseases caused by them. Description With this motivation, we have developed ListeriaBase, a webListeria genomic resource and analysis platform to facilitate comparative analysis ofListeria spp. ListeriaBase currently houses 850, 402 protein-coding genes, 18, 113 RNAs and 15, 576 tRNAs from 285 genome sequences of differentListeria strains. An AJAX-based real time search system implemented in ListeriaBase facilitates searching of this huge genomic data. Our in-house designed comparative analysis tools such as Pairwise Genome Comparison (PGC) tool allowing comparison between two genomes, Pathogenomics Profiling Tool (PathoProT) for comparing the virulence genes, and ListeriaTree for phylogenic classification, were customized and incorporated in ListeriaBase facilitating comparative genomic analysis ofListeria spp. Interestingly, we identified a unique genomic feature in theL. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains ofL. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that theaut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes ofL. monocytogenes . Conclusions ListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis ofListeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses ofL. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available athttp://listeria.um.edu.my .