Assembly breakdown and you will genome suggestions out of K. michiganensis BD177

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 studies and you will phenotypic away from remote filter systems BD177

Restrict parsimony founded and you can limitation probability phylogenetic woods by using the sequence that encodes on 16S rRNA gene showed that brand new closest variety so you’re able to BD177 is actually K. michiganensis and you can K. oxytica (Additional document step 1: Fig. S1, A lot more file dos: Desk S1). Evolutionary divergence range from 16S rRNA gene series ranging from BD177 and you can K. michiganensis E718 are minimum really worth (BD177 compared to K. michiganensis E718: 0.0079) certainly the sequences. Biochemical evaluation were performed on BD177 by API20E to ensure the updates regarding the K. oxytoca and K. michiganensis. Biochemical functions off K. oxytoca ATCC13182(T)(=NCTC13727) and you may K. michiganensis W14(T)(= DSM2544) had been extracted from BacDive Webservices pared with K. oxytoca ATCC13182(T) and you can K. michiganensis W14(T), BD177 is the same having W14 regarding the ?-galactosidase enzyme self-confident and you may urease bad, same that have ATCC13182(T) in arginine dihydrolase positive. Although not, BD177 does not have the employment element regarding citrate since just carbon source, not the same as each other form of challenges (Table 2).

Pan-genome analysis

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 studies off 119 genomes in this studies. Genomes is categorized based on its types annotation regarding the NCBI databases (with the exception of split K. michiganensis BD177). a GC articles of all genomes is actually classified centered on the varieties annotation regarding the NCBI databases. b pie chart of your own 119 reviewed Klebsiella sp. genomes. The bowl-genome cake graph appearing gene blogs visualized by making use of Roary software


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