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).
Restrict parsimony built and you can limit opportunities phylogenetic trees using the sequence one to encodes on 16S rRNA gene showed that the brand new closest kinds to BD177 was K. michiganensis and K. oxytica (Extra file step one: Fig. S1, Most file 2: Dining table S1). Evolutionary divergence range out-of 16S rRNA gene sequence ranging from BD177 and you can K. michiganensis E718 was lowest worthy of (BD177 compared to K. michiganensis E718: 0.0079) among all the https://datingranking.net/tr/edarling-inceleme/ sequences. Biochemical screening was in fact did to your BD177 from the API20E to ensure the position regarding the K. oxytoca and you may K. michiganensis. Biochemical functions off K. oxytoca ATCC13182(T)(=NCTC13727) and you may K. michiganensis W14(T)(= DSM2544) was indeed taken from BacDive Webservices pared having K. oxytoca ATCC13182(T) and you may K. michiganensis W14(T), BD177 is the same which have W14 about ?-galactosidase enzyme confident and you can urease bad, same that have ATCC13182(T) within the arginine dihydrolase positive. Yet not, BD177 doesn’t have the use ability away from citrate due to the fact only carbon origin, different from both types of stresses (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 analysis away from 119 genomes contained in this data. Genomes is categorized based on the species annotation regarding NCBI databases (except for split up K. michiganensis BD177). a beneficial GC posts of all of the genomes are classified centered on their varieties annotation regarding the NCBI database. b cake chart of your 119 analyzed Klebsiella sp. genomes. The latest bowl-genome cake chart showing gene stuff envisioned by making use of Roary app