Installation description and you will genome guidance off K. michiganensis BD177
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 data and phenotypic from isolated strain BD177
Limit parsimony situated and you can limitation probability phylogenetic trees utilizing the series you to encodes towards 16S rRNA gene indicated that the nearest species to BD177 try K. michiganensis and you will K. oxytica (Extra document 1: Fig. S1, A lot more file dos: Table S1). Evolutionary divergence length regarding 16S rRNA gene sequence anywhere between BD177 and you can K. michiganensis E718 is lowest value (BD177 compared to K. michiganensis E718: 0.0079) certainly the sequences. Biochemical evaluating have been did into BD177 from the API20E to verify the standing regarding the K. oxytoca and you will K. michiganensis. Biochemical features out of K. oxytoca ATCC13182(T)(=NCTC13727) and you can K. michiganensis W14(T)(= DSM2544) was taken from BacDive Webservices pared which have K. oxytoca ATCC13182(T) and you will K. michiganensis W14(T), BD177 is similar which have W14 about ?-galactosidase chemical confident and you can urease negative, exact same having ATCC13182(T) for the arginine dihydrolase self-confident. not, BD177 doesn’t always have the use element off citrate given that simply carbon source, unlike each other kind of strains (Desk 2).
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. tamamen Ã¼cretsiz arkadaÅŸlÄ±k siteleri 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 regarding 119 genomes within analysis. Genomes was grouped according to the variety annotation about NCBI databases (except for divide K. michiganensis BD177). an excellent GC stuff of all genomes is labeled predicated on the species annotation regarding NCBI database. b pie chart of your 119 examined Klebsiella sp. genomes. The fresh new bowl-genome pie graph exhibiting gene articles visualized by making use of Roary app