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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 remote strain BD177
Maximum parsimony depending and you will limitation possibilities phylogenetic woods utilizing the succession that encodes to the 16S rRNA gene showed that the latest closest variety in order to BD177 are K. michiganensis and you may K. oxytica (More file step one: Fig. S1, More document dos: Dining table S1). Evolutionary divergence distance from 16S rRNA gene series between BD177 and K. michiganensis E718 is minimal value (BD177 compared to K. michiganensis E718: 0.0079) among the sequences. Biochemical assessment were performed toward BD177 by the API20E to verify its reputation in the K. oxytoca and you may K. michiganensis. Biochemical services out-of K. oxytoca ATCC13182(T)(=NCTC13727) and you can K. michiganensis W14(T)(= DSM2544) have been taken from BacDive Webservices pared having K. oxytoca ATCC13182(T) and K. michiganensis W14(T), BD177 is the same which have W14 regarding ?-galactosidase chemical positive and you may urease bad, same having ATCC13182(T) when you look daddyhunt giriÅŸ at the arginine dihydrolase confident. not, BD177 does not have use feature out-of citrate since just carbon dioxide provider, not the same as both particular strains (Desk 2).
Pan-genome investigation
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 data away from 119 genomes inside research. Genomes was classified centered on its species annotation in the NCBI databases (with the exception of split K. michiganensis BD177). a GC content of all of the genomes try labeled centered on the variety annotation from the NCBI databases. b cake graph of your own 119 assessed Klebsiella sp. genomes. The fresh new bowl-genome pie chart showing gene blogs visualized through the use of Roary software