Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response
- Ten percent of the G. - Conclusions: This analysis offers an overview of the dynamic processes at play in G. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - Full list of author information is available at the end of the article. - Palms are ‘the’ iconic plant species of the tropics.. - Palms are an important part of the social and economic spheres, both globally and locally. - In 2018, palm oil accounted for 40.2% of the world’s vegetable oil production, with 85% of the total palm oil being produced in Malaysia and Indonesia [8].. - Principal component analysis using the transformed normalized counts showed that the first component explained 89% of the variation and clearly separates the transcriptome samples derived from in vitro and in planta growth conditions (Fig. - The three replicates within the in planta group had low variation, with some separation of the G. - A search against the Pfam and NCBI Conserved Domain Database (CDD) databases using the Reverse Position-Specific BLAST (RPS-BLAST) [15], also known as CD-search (Conserved Domain Search), identified protein domains in of the assem- bled transcript loci (Fig. - Table 1 Mapping statistics of the reads aligned to the Ganoderma boninense genome. - contribute to the NCBI-CDD, the use of Pfam database provided annotation for an additional ~ 1.5% of the total as well as differentially expressed transcripts (Fig. - Secreted proteins and CAZymes were identified from predicted protein coding regions (8899) extracted from the RNAseq transcript loci with domain annotations being available for 58.8% of the se- creted proteins and 90.1% CAZymes (Fig. - Approxi- mately of the transcript loci that comprise the in planta DEGs dataset had an annotation and 55.2% of the secreted DEGs and 90.8% of the CAZyme DEGs contained annotated protein domains (Fig. - In the interaction between G. - In the G. - mellea [21], were also up-regulated in G. - A total of of the predicted secreted proteins have an altered expression pattern when G. - 4), including 38 proteins up-regulated in planta. - Three of the secreted lineage-specific proteins were in the top-20 most up-regulated genes during the interaction. - One of the most highly up-regulated genes (log 2 FC = 12.03, p adj = 1.37E-71) is a secreted protein that carries the CFEM domain, which is unique to fungi [22]. - Four S10 (carboxypeptidase Y) including one secreted S10, and three other serine peptidases, S8 (subtilisin), S24 (LexA repressor), and S53 (sedolisin), were up-regulated in planta. - Eleven aspartyl peptidases (APs) including two secreted APs, and five metalloproteases including two M48 (STE24), one each of M1 (membrane alanyl amino- peptidase), M20 (glutamate carboxypeptidase), and M24 (methionyl aminopeptidase 1), were up-regulated in G.. - Two protease families, S8 and M1, are two of the most common peptidase fam- ilies found in fungi [23]. - MFSD8 were up-regulated during interaction in G. - five copies) were up-regulated in planta. - Cellular respiration and carbon catabolite repression All 33 copies of the enzymes that are key in oxidative phosphorylation steps of respiration, including cyto- chrome b, cytochrome c, and cytochrome-related assem- bly proteins were down-regulated in G. - The alter- native oxidase (AOX), a part of the electron transport chain was also down-regulated during the interaction.. - Consistent with this regulation, a majority (80%) of the G. - The RNAseq data acquired in this single time-point pilot study provides a snapshot of the differentially expressed transcripts during G. - the one analyzed in this study, had replicated measures of the transcriptional changes that occur during G. - However, wood decay fungi act slowly, and it is likely that early sampling of the inter- action might not reveal much about the transcriptional changes occurring during host colonization. - RNAseq data- sets that comprise of a single time-point at 4 weeks are more likely to reveal components of the host colonization process than multiple early time-points. - Analysis of the transcriptome and proteome data showed that pres- ence of glucose repressed the expression of ~ 7% genes, primarily CAZymes and carbon catabolic genes, in D.. - In the current DEGs dataset, 28 (80%) of the in planta expressed glycosyl hydrolases, that target cellulose and hemicellulose components of plant cell wall, were down-regulated when G. - The online version contains supplementary material available at https://doi.. - org/10.1186/s . - Any opinions, findings, conclu- sions, or recommendations expressed in this publication are those of the au- thor(s) and do not necessarily reflect the view of the National Institute of Food and Agriculture (NIFA) or the United States Department of Agriculture (USDA). - Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily re- flect the views of the funding agency. - Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. - 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