Development of ListeriaBase and comparative analysis of Listeria monocytogenes

BMC Genomics

Database

Avirup Dutta¹  Naresh VR Mutha¹  Cheuk Chuen Siow¹  Hamed Heydari²  Wei Yee Wee³  Shi Yang Tan³  Mia Yang Ang³  Mui Fern Tan³  Guat Jah Wong³  Siew Woh Choo⁴ 

[1] Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603, Kuala Lumpur, Malaysia;Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603, Kuala Lumpur, Malaysia;Computer Science and Engineering Department, University of Nebraska-Lincoln, 1468588-0115, Lincoln, NE, USA;Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603, Kuala Lumpur, Malaysia;Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia;Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603, Kuala Lumpur, Malaysia;Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia;Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, 50603, Kuala Lumpur, Malaysia;

关键词: ListeriaBase;    Listeria;    Comparative analysis;   

DOI  :  10.1186/s12864-015-1959-5

 received in 2015-07-15, accepted in 2015-09-29,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundListeria 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. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them.DescriptionWith this motivation, we have developed ListeriaBase, a web Listeria genomic resource and analysis platform to facilitate comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria 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 of Listeria spp. Interestingly, we identified a unique genomic feature in the L. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains of L. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that the aut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes of L. monocytogenes.ConclusionsListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis of Listeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses of L. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available at http://listeria.um.edu.my.

【 授权许可】

CC BY   
© Tan et al. 2015