Computational protocol: Complete Genome Sequence of Wohlfahrtiimonas chitiniclastica Strain BM-Y, Isolated from the Pancreas of a Zebra in China

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Protocol publication

[…] Wohlfahrtiimonas chitiniclastica, the type species of the Wohlfahrtiimonas genus, is a Gram-negative bacillus with close phylogeny to Ignatzschineria larvae, and is also a pathogen of myiasis in homeless adults, Odocoileus virginianus, and cattle (). Although the pathogenesis of W. chitiniclastica associated disease has not been interpreted completely, the fly Wohlfahrtia magnifica acting as a carrier of W. chitiniclastica and wound contamination was believed to be the key factor of bacterial septicemia (). To date, five Wohlfahrtiimonas species and no more than 20 W. chitiniclastica strains have been isolated in the world. Of these, only antibiotic sensitive strain SH04 has been sequenced completely in China ().Given that W. chitiniclastica can cause severe infections in clinics and threaten the health of humans and animals, here, we report and analyze the complete genome sequence of W. chitiniclastica strain BM-Y, which was isolated from the pancreas of a zebra in China. BM-Y carried a blaVEB-1 gene cassette resistant to ceftazidime, ampicillin, tetracycline, etc. These characterizations were found in W. chitiniclastica first.Whole-genome sequencing of W. chitiniclastica strain BM-Y was performed using a PacBio RS II system with a 20-kb library and C4-P6 chemistry. A total of 187,537 long circular reads (314-fold coverage) with an average length of 3,670 bp and 82.6% estimated accuracy were used as input for genome de novo assembly by single-molecule real-time (SMRT) analysis pipeline v2.3.0 in conjunction with RS_HGAP_Assembly3 protocol (). Prediction and annotation of coding sequences were conducted with Glimmer software, Swiss-Prot, KEGG, COG, and GenBank nr databases. Transfer RNAs (tRNAs) were predicted using tRNAscan-SE () and ribosomal RNAs (rRNAs) were predicted using RNAmmer (). Gene content was analyzed using BLASTp with parameters of more than 50% sequence identity and an e-value cutoff of less than 1e−5. Whole chromosome alignment and comparison was conducted with MUMmer3 ().The genome of W. chitiniclastica strain BM-Y consisted of a chromosome of 2,181,980 bp (two contigs) with 43.50% G+C content. Preliminary draft annotation indicates that the genome is predicted to contain 2,085 genes encoding for 1,856 proteins and 55 for tRNA. Reciprocal average nucleotide identity (ANI index) between BM-Y and two reference strains, SH04 and DSM18708, reveals that BM-Y shares 98.20% and 97.05% identity with SH04 and DSM18708, respectively, while SH04 and DSM18708 share 97.21% identity. Furthermore, BM-Y chromosome alignments at the nucleotide level with genomes of strains SH04 and DSM18708 reveal large chromosome inversions and rearrangements; the blaVEB-1 gene cassette is contained within contig2. […]

Pipeline specifications

Software tools SMRT-Analysis, Glimmer, tRNAscan-SE, RNAmmer, BLASTP, MUMmer
Databases UniProt KEGG
Applications Genome annotation, Phylogenetics, WGS analysis, Nucleotide sequence alignment
Chemicals Ampicillin, Ceftazidime, Tetracycline