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 phenotypic of remote filters BD177
Restriction parsimony mainly based and you will maximum likelihood phylogenetic trees using the sequence one to encodes into 16S rRNA gene indicated that the new nearest species so you can BD177 is K. michiganensis and K. oxytica (A lot more document step 1: Fig. S1, A lot more document 2: Dining table S1). Evolutionary divergence range of 16S rRNA gene sequence between BD177 and K. michiganensis E718 is minimum well worth (BD177 compared to K. michiganensis E718: 0.0079) certainly one of all sequences. Biochemical tests was in fact performed towards BD177 of the API20E to verify their status throughout the K. oxytoca and you will K. michiganensis. Biochemical functions off K. oxytoca ATCC13182(T)(=NCTC13727) and you may K. michiganensis W14(T)(= DSM2544) was indeed extracted from BacDive Webservices pared that have K. oxytoca ATCC13182(T) and you will K. michiganensis W14(T), BD177 is similar with W14 throughout the ?-galactosidase enzyme confident and you may urease bad, same having ATCC13182(T) for the arginine dihydrolase self-confident. Although not, BD177 does not have the employment element regarding citrate due to the fact simply carbon provider, unlike each other types of stresses (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) Bu sayfayı ziyaret edin. 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 analysis out-of 119 genomes inside analysis. Genomes was categorized predicated on its kinds annotation on NCBI databases (with the exception of divide K. michiganensis BD177). good GC articles of all the genomes is grouped centered on their types annotation regarding NCBI databases. b pie graph of your own 119 analyzed Klebsiella sp. genomes. This new dish-genome pie chart showing gene content envisioned by making use of Roary application
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