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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 research and you may phenotypic out of remote filters BD177
Maximum parsimony based and you can maximum chances phylogenetic trees utilizing the succession that encodes towards 16S rRNA gene showed that the closest kinds to help you BD177 is K. michiganensis and K. oxytica (A lot more file step one: Fig. S1, A lot more document dos: Dining table S1). Evolutionary divergence length regarding 16S rRNA gene succession between BD177 and K. michiganensis E718 is lowest well worth (BD177 against K. michiganensis E718: 0.0079) one of all the sequences. Biochemical evaluation was basically did on BD177 by the API20E to ensure their position about K. oxytoca and you will K. michiganensis. Biochemical features regarding K. oxytoca ATCC13182(T)(=NCTC13727) and K. michiganensis W14(T)(= DSM2544) had been extracted from BacDive Webservices pared that have K. oxytoca ATCC13182(T) and you can K. michiganensis W14(T), BD177 is the identical which have W14 throughout the ?-galactosidase enzyme positive and you can urease negative, same which have ATCC13182(T) inside the arginine dihydrolase positive. not, BD177 doesn’t always have the employment ability regarding citrate due to the fact simply carbon resource, distinctive from each other sort of strains (Desk 2).
Pan-genome analysis
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 investigation out of 119 genomes within study. Genomes is labeled centered on its types annotation from the NCBI databases (except for split K. michiganensis BD177). an effective GC content of the many genomes are classified according to its kinds annotation kasidie üyelik on the NCBI database. b pie graph of the 119 reviewed Klebsiella sp. genomes. This new dish-genome cake chart proving gene stuff envisioned by using Roary app