Additional file 3: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Putative active genes misidentified as pseudogenes due to assembly errors. (PDF 210 kb

Additional file 4: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Circular plots showing average coverage of the genome by RNA-Seq reads in all six time points. The outermost and the second outermost circles represent positions of genes on the forward (red) and reverse (blue) strands respectively. The third circle (green) stands for pseudogenes. The yellow peak and shading area represents transcription greater than the average and violet lower than average. Floating window of 10,000 bp with step of 200 bp was used to render the shading area. (PDF 701 kb

Additional file 6: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Differential expression analysis. Complete results of differential expression analysis using DESeq2. (XLSX 2287 kb

Additional file 8: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

COG functional categories of differential expressed genes. Barplots showing the number of COG categories associated with differentially expressed genes between adjacent time points. (PDF 226 kb

Additional file 2: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Silent pseudogenes. (PDF 195 kb

Additional file 5: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Differential analysis of adjacent time points using MA plots. MA plots showing statistically differentially expressed genes in color. Color coding respect the color coding used in Venn diagrams in Fig. 4. (PDF 315 kb

Additional file 7: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Dotplot of C. beijerinckii NRRL B-598 and C. beijerinckii NCIMB 8052 genome. Dotplots showing that no major rearrangement between the two strains are present. (PDF 315 kb

Additional file 1: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Snapshots from microscopic observation during cultivation. (PDF 628 kb

Data_Sheet_1_Whole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.).docx

BackgroundThis paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth.MethodsP. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out.Results and discussionThe typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.</p