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 study and you can phenotypic away from remote strain BD177
Limit parsimony oriented and you will restriction probability phylogenetic woods utilising the series that encodes on 16S rRNA gene showed that new closest kinds in order to BD177 was K. michiganensis and you may K. oxytica (Most file 1: Fig. S1, A lot more file dos: Table S1). Evolutionary divergence point from 16S rRNA gene succession between BD177 and you will K. michiganensis E718 was lowest worthy of (BD177 compared to K. michiganensis E718: 0.0079) one of all the sequences. Biochemical evaluating have been did for the BD177 by the API20E to ensure their condition regarding K. oxytoca and you will K. michiganensis. Biochemical qualities out-of K. oxytoca ATCC13182(T)(=NCTC13727) and you may K. michiganensis W14(T)(= DSM2544) was basically obtained from BacDive Webservices pared having K. oxytoca ATCC13182(T) and you will K. michiganensis W14(T), BD177 is the same that have W14 from the ?-galactosidase enzyme positive and you can urease bad, same having ATCC13182(T) inside arginine dihydrolase positive. But not, BD177 doesn’t have the utilization function of citrate as just carbon dioxide supply, distinct from both method of strains (Desk 2).
Pan-genome studies
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 chatrandom Hesap Nasıl Silme 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 studies away from 119 genomes within data. Genomes was categorized considering their varieties annotation about NCBI databases (with the exception of divide K. michiganensis BD177). a good GC blogs of all of the genomes try categorized considering their variety annotation regarding the NCBI database. b cake chart of 119 reviewed Klebsiella sp. genomes. The latest dish-genome pie chart demonstrating gene stuff visualized with the use of Roary app