Assembly malfunction and genome suggestions away from K. michiganensis BD177
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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 phenotypic from isolated strain BD177
Limitation parsimony dependent and you can limitation opportunities phylogenetic woods making use of the series you to definitely encodes to your 16S rRNA gene showed that new closest kinds to help you BD177 are K. michiganensis and K. oxytica (Additional file step one: Fig. S1, Even more document dos: Table S1). Evolutionary divergence distance of 16S rRNA gene sequence anywhere between BD177 and you can K. michiganensis E718 was minimum value (BD177 vs K. michiganensis E718: 0.0079) one of every sequences. Biochemical screening was performed towards BD177 because of the API20E to confirm their position from the K. oxytoca and K. michiganensis. Biochemical attributes out of K. oxytoca ATCC13182(T)(=NCTC13727) and K. michiganensis W14(T)(= DSM2544) was indeed taken from BacDive Webservices pared which have K. oxytoca ATCC13182(T) and you will K. michiganensis W14(T), BD177 is the same with W14 on ?-galactosidase enzyme self-confident and you may urease bad, exact same that have ATCC13182(T) into the arginine dihydrolase positive. Although not, BD177 doesn’t have use feature off citrate given that just carbon provider, unlike both form of stresses (Dining table dos).
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 analysis of 119 genomes inside research. Genomes was grouped predicated on its variety annotation regarding the NCBI databases (except for split up K. michiganensis BD177). an effective GC stuff of all the genomes try categorized based on its species annotation regarding NCBI database. b pie chart of 119 reviewed Klebsiella sp. genomes. This new dish-genome pie chart demonstrating gene blogs visualized by making use of Roary app