Computational protocol: Genome analysis of Listeria ivanovii strain G770 that caused a deadly aortic prosthesis infection

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Protocol publication

[…] The reads obtained after sequencing were assembled using the A5 assembler . Then a finishing step was performed with the Mauve aligner software and CLC bioserver . After assembly and finishing, the size of the genome was 2.9 Mb. Open reading frames (ORFs) were predicted by Prodigal software ( with default parameters. Functional annotation was done by comparison of ORF sequences to the GenBank and Clusters of Orthologous Groups (COGs) database using BLASTP. tRNAs and rRNAs were detected using tRNAscan-SE v.1.21 and RNAmmer 1.2 , respectively.The absence of plasmids was verified both by searching the gene annotation for any plasmid-related gene and by mapping all contigs against previously published Listeria plasmid sequences.To identify the most closely related L. ivanovii genomes, we performed a phylogenetic analysis () by comparing the sequences of the hlyA gene using the neighbour-joining method and MEGA 6 software . Subsequently we compared the genomic content of strain G770 and those of the most closely related L. ivanovii strains available in GenBank. The genome sequence similarity between studied strains was evaluated with GGDC software ( analysis of virulence factors was performed by searching the genes already identified as responsible for virulence in L. ivanovii (six genes of the LIPI-1 cluster, internalin genes, genes of stress survival islet 1 (SS1)) and by screening every gene that was specific to strain G770 for a putative role in virulence. The CRISPRFinder algorithm was used to identify putative CRISPR (clustered regularly interspaced short palindromic repeat) loci . […]

Pipeline specifications

Software tools Mauve, BLASTP, tRNAscan-SE, RNAmmer, MEGA, GGDC, CRISPRFinder
Applications Genome annotation, Phylogenetics, Nucleotide sequence alignment
Organisms Listeria ivanovii, Homo sapiens
Diseases Infection