Installation breakdown and you may genome information 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 analysis and you will phenotypic off remote filters BD177
Restriction parsimony based and you may limit possibilities phylogenetic trees by using the series you to definitely encodes toward 16S rRNA gene revealed that the brand new nearest varieties so you’re able to BD177 are K. michiganensis and you may K. oxytica (More document step 1: Fig. S1, Even more file dos: Table S1). Evolutionary divergence range away from 16S rRNA gene series ranging from BD177 and K. michiganensis E718 try minimum well worth (BD177 against K. michiganensis E718: 0.0079) among every sequences. Biochemical screening were did with the BD177 from the API20E to verify burada bul their condition regarding the K. oxytoca and K. michiganensis. Biochemical properties away from K. oxytoca ATCC13182(T)(=NCTC13727) and you will K. michiganensis W14(T)(= DSM2544) was in fact obtained from BacDive Webservices pared having K. oxytoca ATCC13182(T) and you will K. michiganensis W14(T), BD177 is similar with W14 from the ?-galactosidase enzyme self-confident and you may urease bad, same which have ATCC13182(T) into the arginine dihydrolase confident. not, BD177 does not have the use feature of citrate since the simply carbon origin, distinctive from one another style of stresses (Dining table 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. 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 data out of 119 genomes within research. Genomes is grouped centered on its varieties annotation from the NCBI databases (apart from split K. michiganensis BD177). a beneficial GC content of all the genomes was grouped considering the variety annotation on NCBI databases. b pie graph of your 119 examined Klebsiella sp. genomes. Brand new bowl-genome pie graph showing gene blogs envisioned through the use of Roary app