Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

Abstract

BackgroundApple canker is a devastating branch disease caused by Valsa mali (Vm). The endophytic actinomycete Saccharothrix yanglingensis Hhs.015 (Sy Hhs.015) can effectively inhibit the growth of Vm. To reveal the mechanism, by which Vm respond to Sy Hhs.015, the transcriptome of Vm was analyzed using RNA-seq technology.ResultsCompared with normal growing Vm in the control group, 1476 genes were significantly differentially expressed in the Sy Hhs.015’s treatment group, of which 851 genes were up-regulated and 625 genes were down-regulated. Combined gene function and pathway analysis of differentially expressed genes (DEGs) revealed that Sy Hhs.015 affected the carbohydrate metabolic pathway, which is utilized by Vm for energy production. Approximately 82% of the glycoside hydrolase genes were down-regulated, including three pectinase genes (PGs), which are key pathogenic factors. The cell wall structure of Vm was disrupted by Sy Hhs.015 and cell wall-related genes were found to be down-regulated. Of the peroxisome associated genes, those encoding catalase (CAT) and superoxide dismutase (SOD) which scavenge reactive oxygen species (ROS), as well as those encoding AMACR and ACAA1 which are related to the β-oxidation of fatty acids, were down-regulated. MS and ICL, key genes in glyoxylate cycle, were also down-regulated. In response to the stress of Sy Hhs.015 exposure, Vm increased amino acid metabolism to synthesize the required nitrogenous compounds, while alpha-keto acids, which involved in the TCA cycle, could be used to produce energy by deamination or transamination. Retinol dehydrogenase, associated with cell wall dextran synthesis, and sterol 24-C-methyltransferase, related to cell membrane ergosterol synthesis, were up-regulated. The genes encoding glutathione S-transferase, (GST), which has antioxidant activity and ABC transporters which have an efflux function, were also up-regulated.ConclusionThese results show that the response of Vm to Sy Hhs.015 exposure is a complicated and highly regulated process, and provide a theoretical basis for both clarifying the biocontrol mechanism of Sy Hhs.015 and the response of Vm to stress.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1225-5) contains supplementary material, which is available to authorized users.

Biocontrol and Action Mechanism of Bacillus amyloliquefaciens and Bacillus subtilis in Soybean Phytophthora Blight

“…The GO enrichment analysis describes the classification of gene functions and the relationships between these genes. The GO functions of DEGs were divided into three groups: The biological process, the cellular component, and the molecular function [26,27]. In the BST samples, 217 up-regulated and 242 down-regulated differentially expressed genes were annotated, respectively.…”

“…In the molecular functional classification, DEGs are enriched in nucleoside binding, transferase activity, the transfer of phosphorus-containing groups, and hydrolase activity. Transcriptome analysis was also occasionally applied to the study of biological control mechanisms [26,27]. Rhizoctonia solani was treated with the Serratia proteamaculans and S. plymuthica , resulting in a difference of 462 and 242 genes, respectively, and these gene enrichment assays and functional classification of DEGs were annotated by the GO term [26].…”

“…The transcriptome revealed that most of the glycoside hydrolase genes were down-regulated, including three key causative genes and the pectinase gene. The GO term revealed that the DEGs were down-regulated and involved in the dcatalytic activity, transmembrane transport, and hydrolase activity [27]. A transcriptome analysis was carried out to mine the downstream genes, whose expression levels were affected by melatonin [28].…”

“…Transcriptome analysis was also occasionally applied to the study of biological control mechanisms [26,27]. Our research uses transcriptomics to elucidate the response of P. sojae under the stress of B. amyloliquefaciens and B. subtilis , and this will contribute to the biological control molecular mechanism of P. sojae and lead to an in-depth understanding of the interactions between rhizosphere bacterial and soil-borne oomycete pathogens.…”

Investigation on the Antifungal Ingredients of Saccharothrix Yanglingensis Hhs.015, an Antagonistic Endophytic Actinomycete Isolated from Cucumber Plant

“…The inhibition effect of WH01 on hyphae of V. mali was designed according to Liu and Fan et al [27] descriptions. The V. mali stored at −80 °C were cultured in PDA medium for 48 hours, and then transferred to the center of the other PDA solid medium.…”