Additional file 4: Figure S1. of Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

A) Comparison of the genomic distribution of lincRNAs and protein-coding genes across the 12 potato chromosomes. The outer grey track represents the 12 potato chromosomes, with a scale (Mb) showing the length of each chromosome. The red histograms (second track with an outer orientation) and blue histograms (third track with inner orientation) represent the abundance and distribution of mRNA and lincRNAs, respectively, throughout the potato genome. The bin size (histogram width) = 5 Mbp). B) Comparison of LincRNA lengths to protein-coding mRNA transcripts in potato (PGSC_DM_v4.03 genome assembly). (PDF 258 kb

Rubus lambertianus Ser.

原著和名: シマバライチゴ科名: バラ科 = Rosaceae採集地: 長崎県 島原市 眉山 (肥前 島原市 眉山)採集日: 1975/1/3採集者: 萩庭丈壽整理番号: JH009571国立科学博物館整理番号: TNS-VS-95957

Additional file 2: Table S6. of Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

List of RT-PCR primers used in this study. (XLSX 8 kb

Chloranthus glaber Makino

原著和名: センリャウ科名: センリョウ科 = Chloranthaceae採集地: 千葉県 千葉市 千葉大学 (下総 千葉市 千葉大学)採集日: 1971/5/27採集者: 萩庭丈壽整理番号: JH008984国立科学博物館整理番号: TNS-VS-95898

KEGG pathway analysis of <i>P</i>. <i>atrosepticum</i> genes up- and down-regulated in cross-protected cells compared to growing ones (p-value ≤0.05).

<p>KEGG pathway analysis of <i>P</i>. <i>atrosepticum</i> genes up- and down-regulated in cross-protected cells compared to growing ones (p-value ≤0.05).</p

Cross-protective effect in <i>P</i>. <i>atrosepticum</i> SCRI1043 cells during starvation.

<p><i>Pba</i> cells of late log growth phase were transferred to carbon-deficient medium (primary stress). To elucidate the dynamics of the formation of cross-protected phenotype during starvation induced stress, <i>Pba</i> cells after 0, 4, 8, 24 and 48 h of starvation were subjected to secondary stresses: 50°C for 5 min (white columns), 2.5 mM H₂O₂ for 1 h (gray columns) or 20% NaCl for 1 h (black columns). Cells were plated prior to and right after secondary stresses. The survival of cells starving for 0, 4, 8, 24 and 48 h was assessed by the comparison of cell titer prior and after secondary stress factor exposure. Values are the average ± SD of three biological replicates.</p

Global Gene Expression Analysis of Cross-Protected Phenotype of <i>Pectobacterium atrosepticum</i>

<div><p>The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, <i>Pectobacterium atrosepticum</i> (<i>Pba</i>) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed <i>Pba</i> to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected <i>Pba</i> phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features that distinguish cross-protected phenotype from the growing cells.</p></div

Modules and pathways of genes expressed differentially in <i>P</i>. <i>atrosepticum</i> during growth in nutrient rich medium and after the formation of cross-protected phenotype under starvation conditions.

<p>Manually assigned modules and pathways are marked with stars.</p

Summary of RNA-seq reads mapping to reference genes.

<p>Summary of RNA-seq reads mapping to reference genes.</p

Number of DEGs assigned to a particular pathway by means of GO, KEGG and manual classification using different databases.

<p>Number of DEGs assigned to a particular pathway by means of GO, KEGG and manual classification using different databases.</p