۱٫۳ 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).
۱۶S rRNA phylogenetic analysis and phenotypic of isolated strain BD177
Limitation parsimony established and you can restrict chances phylogenetic woods utilizing the succession that encodes towards the 16S rRNA gene indicated that the fresh closest variety so you can BD177 are K. michiganensis and you may K. oxytica (Even more file step 1: Fig. S1, Even more document dos: Table S1). Evolutionary divergence length off 16S rRNA gene succession between BD177 and you will K. michiganensis E718 is actually minimum well worth (BD177 compared to K. michiganensis E718: 0.0079) among the sequences. Biochemical assessment was performed towards BD177 by API20E to confirm the reputation throughout the K. oxytoca and you can K. michiganensis. Biochemical properties out-of K. oxytoca ATCC13182(T)(=NCTC13727) and K. michiganensis W14(T)(= DSM2544) was indeed taken from BacDive Webservices pared having K. oxytoca ATCC13182(T) and you can K. michiganensis W14(T), BD177 is similar having W14 about ?-galactosidase enzyme self-confident and you can urease negative, exact same with ATCC13182(T) inside the arginine dihydrolase self-confident. However, BD177 does not have use ability out of citrate because merely carbon resource, not the same as one another kind of strains (Table 2).
In this study, we considered the 128 publicly available genome assemblies for the Klebsiella sp. (Additional file 3: Table S2). www.datingranking.net/tr/eastmeeteast-inceleme/ 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 regarding 119 genomes within this study. Genomes is actually classified based on its types annotation on NCBI databases (except for divide K. michiganensis BD177). a beneficial GC stuff of the many genomes is labeled predicated on its varieties annotation on the NCBI databases. b cake chart of your own 119 analyzed Klebsiella sp. genomes. The bowl-genome cake chart appearing gene content envisioned with the use of Roary software