1.3 Gbp) were processed to remove SMRT bell adapters, short and low-quality reads (< 80% accuracy) using SMRT Analysis version 2.3 ( A total of 155,828 filtered reads (average length, 8.9 Kb) were used for de novo assembly using Celera Assembler , with self-correction of the PacBio reads. A total of 1091 Mb paired-end Illumina reads screened from a 500-bp genomic library were mapped using SOAP to the bacterial plasmid database for tracing the presence of any plasmid and filling the gaps. The de novo assembly resulted in five contigs, representing the K. michiganensis BD177 complete genome of 6,812,698 bp with GC content % in a single chromosome and four plasmids. The annotated genome contains 6714 genes, 25rRNA genes, and 86 tRNA genes (Table 1).
Maximum parsimony founded and maximum chances phylogenetic trees using the series you to encodes to your 16S rRNA gene indicated that the closest varieties so you’re able to BD177 was K. michiganensis and K. oxytica (A lot more document step one: Fig. S1, Even more document 2: Table S1). Evolutionary divergence point from 16S rRNA gene series ranging from BD177 and you can K. michiganensis E718 are lowest value dominicancupid kuponu (BD177 against K. michiganensis E718: 0.0079) among the sequences. Biochemical tests were performed towards the BD177 by the API20E to verify the standing regarding K. oxytoca and K. michiganensis. Biochemical features from K. oxytoca ATCC13182(T)(=NCTC13727) and you may K. michiganensis W14(T)(= DSM2544) were extracted from BacDive Webservices pared having K. oxytoca ATCC13182(T) and K. michiganensis W14(T), BD177 is the identical which have W14 on the ?-galactosidase enzyme confident and you may urease bad, exact same with ATCC13182(T) inside the arginine dihydrolase self-confident. Yet not, BD177 does not have the use ability out-of citrate once the merely carbon dioxide supply, distinctive from both method of strains (Dining table dos).
In this study, we considered the 128 publicly available genome assemblies for the Klebsiella sp. (Additional file 3: Table S2). Of these genomes, 26 were originally annotated as K. aerogenes, 13 were K. michiganensis, 27 were K. oxytoca, and 15 were K. pneumoniae. 25 were K. quasipneumoniae, 1 was K. quasivariicola, 21 were K. variicola. The type strain genome of each species is included in these genomes. These genome assemblies were passed strict quality control (N75 values of > 10,000 bp, < 500 undetermined bases per 100,000 bases, > 90% completeness and < 5% contamination) by quast and checkm (Additional file 4: Table S3). This resulted in a total of 118 Klebsiella sp. strains studied, where ten low-quality genome assemblies were discarded. The GC contents of the species K. michiganensis, K. oxytoca, K. pneumoniae, K. variicola, and K. quasipneumoniae showed low intraspecies variation, with respective average values of , , , and % (Fig. 1a), whereas larger interspecies diversity was observed. In contrast, K. aerogenes genomes can be divided into two groups, a large group showing a GC content in the range of that of Klebsiella aerogenes ( to %) and a small group of two genomes ( and %) showing a much greater GC content, similar to that of the K. pneumoniae, K.variicola and K. quasipneumoniae genomes (respective average values about 57%). Based on GC content of the genome, K. pneumoniae, K.variicola, K. quasivariicola, and K. quasipneumoniae were considered as a high GC group content, and K. michiganensis and K. oxytoca were considered as a low GC content group. The genome sequence of our new isolate, which we designated K. michiganensis BD177 with % GC content (Table 1), shows a similar to that of the low GC content Klebsiella sp. group (Fig. 1a).
Pan-genome study out-of 119 genomes contained in this analysis. Genomes is grouped predicated on their types annotation on NCBI database (with the exception of split K. michiganensis BD177). an excellent GC posts of all of the genomes is categorized according to the kinds annotation on the NCBI database. b cake chart of one’s 119 reviewed Klebsiella sp. genomes. The newest pan-genome pie graph showing gene stuff visualized using Roary software
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