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).
Restriction parsimony oriented and you can maximum likelihood phylogenetic trees by using the series that encodes with the 16S rRNA gene showed that the new closest types in order to BD177 are K. michiganensis and K. oxytica (Additional file 1: Fig. S1, A lot more file dos: Dining table S1). Evolutionary divergence distance out-of 16S rRNA gene succession anywhere between BD177 and you can K. michiganensis E718 was minimal worthy of (BD177 versus K. michiganensis E718: 0.0079) certainly one of the sequences. Biochemical evaluation was basically performed on BD177 because of the API20E to confirm the standing regarding K. oxytoca and you may K. michiganensis. Biochemical functions away from K. oxytoca ATCC13182(T)(=NCTC13727) and you can K. michiganensis W14(T)(= DSM2544) was indeed taken from BacDive Webservices pared with K. oxytoca ATCC13182(T) and K. michiganensis W14(T), BD177 is similar which have W14 in the ?-galactosidase enzyme confident and you can urease negative, same which have ATCC13182(T) within the arginine dihydrolase self-confident. not, BD177 doesn’t always have the utilization ability away from citrate because the only carbon dioxide source, not the same as each other sorts of challenges (Desk 2).
In this study, we considered the https://datingranking.net/tr/heated-affairs-inceleme 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 research of 119 genomes in this investigation. Genomes was classified centered on their kinds annotation in the NCBI database (apart from split K. michiganensis BD177). a good GC stuff of all the genomes was categorized predicated on their species annotation in the NCBI database. b cake graph of one’s 119 reviewed Klebsiella sp. genomes. This new dish-genome cake chart indicating gene content envisioned with the use of Roary application