Overall performance
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 you may phenotypic from remote filters BD177
Limit parsimony founded and you will restriction chances phylogenetic woods making use of the series you to encodes on the 16S rRNA gene revealed that the brand new closest kinds so you’re able to BD177 are K. michiganensis and you will K. oxytica (Even more file 1: Fig. S1, Even more document 2: Table S1). Evolutionary divergence point from 16S rRNA gene succession between BD177 and you may K. michiganensis E718 are minimum really worth (BD177 vs K. michiganensis E718: 0.0079) one of all sequences. Biochemical evaluation was in fact performed towards the BD177 by the API20E to ensure its reputation on the K. oxytoca and you may K. michiganensis. Biochemical attributes regarding K. oxytoca ATCC13182(T)(=NCTC13727) and you can K. michiganensis W14(T)(= DSM2544) was extracted from BacDive Webservices pared with K. oxytoca ATCC13182(T) and K. michiganensis W14(T), BD177 is the same having W14 from the ?-galactosidase chemical positive and you will urease negative, exact same which have ATCC13182(T) inside arginine dihydrolase confident. Yet not, BD177 doesn’t have the utilization element away from citrate because the only carbon dioxide resource, unlike both method of challenges (Table 2).
Pan-genome study
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 research of 119 genomes in this data. Genomes are categorized according to their kinds annotation about NCBI database (except for split K. michiganensis BD177). an effective GC posts of all genomes try categorized based on its types annotation in the NCBI database. b cake chart of 119 assessed Klebsiella sp. genomes. The brand new datingranking.net/tr/bronymate-inceleme bowl-genome cake chart demonstrating gene stuff visualized using Roary app
