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).
16S rRNA phylogenetic investigation and you can phenotypic out-of remote strain BD177
Maximum parsimony dependent and you will restrict opportunities phylogenetic trees making use of the sequence one to encodes to your 16S rRNA gene indicated that the fresh closest variety in order to BD177 was K. michiganensis and you can K. oxytica (A lot more document step 1: Fig. S1, Even more document dos: Dining table S1). Evolutionary divergence range out of 16S rRNA gene series between BD177 and you can K. michiganensis E718 is minimal value (BD177 vs K. michiganensis E718: 0.0079) certainly all sequences. Biochemical screening had been did into BD177 because of the API20E to verify its status in the K. oxytoca and you can K. michiganensis. Biochemical properties out-of K. oxytoca ATCC13182(T)(=NCTC13727) and you http://www.datingranking.net/tr/chat-zozo-inceleme/ will K. michiganensis W14(T)(= DSM2544) have been obtained from BacDive Webservices pared that have K. oxytoca ATCC13182(T) and you may K. michiganensis W14(T), BD177 is the same with W14 on ?-galactosidase enzyme confident and you will urease negative, same with ATCC13182(T) in the arginine dihydrolase confident. Yet not, BD177 doesn’t always have the use element out-of citrate since the merely carbon dioxide source, distinct from one another sorts of challenges (Desk 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, 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 data from 119 genomes within research. Genomes are categorized predicated on its variety annotation in the NCBI databases (except for split up K. michiganensis BD177). a great GC content of the many genomes is actually labeled centered on their species annotation in the NCBI databases. b pie graph of the 119 analyzed Klebsiella sp. genomes. The new pan-genome pie graph showing gene posts envisioned using Roary software