Abilities
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 phenotypic out-of isolated filter systems BD177
Restrict parsimony based and limitation possibilities phylogenetic woods using the succession you to definitely encodes on the 16S rRNA gene indicated that brand new closest variety so you’re able to BD177 was K. michiganensis and you will K. oxytica (A lot more file step 1: Fig. S1, Even more document dos: Desk S1). Evolutionary divergence distance away from 16S rRNA gene series ranging from BD177 and you can K. michiganensis E718 is actually minimal well worth (BD177 vs K. michiganensis E718: 0.0079) certainly one of the sequences. Biochemical evaluation had been performed with the BD177 from the API20E to ensure their standing in the K. oxytoca and K. michiganensis. Biochemical qualities away from K. oxytoca ATCC13182(T)(=NCTC13727) and K. michiganensis W14(T)(= DSM2544) was basically extracted from BacDive Webservices pared having K. oxytoca ATCC13182(T) and you will K. michiganensis W14(T), BD177 is similar having W14 about ?-galactosidase chemical self-confident and you will urease bad, same with ATCC13182(T) inside arginine dihydrolase self-confident. But not, BD177 doesn’t always have the employment function off citrate since only carbon dioxide origin, unlike both style of challenges (Dining table dos).
Pan-genome studies
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 in this research. Genomes is actually classified predicated on its kinds annotation from the NCBI databases (with Daha fazla bilgi için tıklayın the exception of split up K. michiganensis BD177). good GC content of the many genomes is actually classified centered on its species annotation regarding the NCBI databases. b pie chart of one’s 119 examined Klebsiella sp. genomes. This new dish-genome pie chart indicating gene stuff envisioned using Roary app