Molecular analysis of the interaction between white rot pathogen (Rigidoporus microporus) and rubber tree (Hevea brasiliensis)
Year: 2016
Type: dissertation
Abstract: The white rot pathogen, Rigidoporus microporus (Basidiomycota) syn. Rigidoporus lignosus is the most destructive root pathogen in rubber plantations located in South East Asia and Africa. Most management practices for the disease have been carried out without adequate knowledge of the population genetics of the pathogen. Our primary objective in the first part of this work was to characterize isolates from rubber trees (Hevea brasiliensis) in Nigeria. The lack of global studies comparing isolates from Asia and Africa where the majority of rubber plantations are located necessitated extending our molecular phylogeny studies to include isolates from other regions of the world. We compared the Nigerian isolates with isolates from South East Asia and Central/South America. Forty isolates were analyzed by sequencing four gene regions: the nuclear ribosomal DNA ITS and LSU, β-tubulin and translation elongation factor 1-α (tef1) genes. The isolates form three distinctive clades corresponding to Africa, South East Asia and South/Central America. There was high intra-species variation within each clade, but no geographic pattern was detected among the Nigerian isolates and also among the West and Central African isolates. Our multi-gene molecular phylogenetic analysis suggests the presence of two distinctive species associated with the white rot disease. Phylogenetic analysis also placed the Rigidoporus genus within the Oxyporus clade of the Hymaenochataeles. This study supports the need for a thorough revision of the Rigidoporus genera within the Polyporales/Hymaenochataeles. To gain insights on the saprotrophic abilities of Rigidoporus microporus isolates associated with the white rot disease of rubber trees, we performed wood decay tests of selected isolates on rubber wood blocks. We included a non-pathogenic endophytic South American isolate for comparative analysis. The structural alterations caused due to fungal growth in the rubber wood blocks was also studied. The pathogenic isolates associated with rubber trees significantly decayed the rubber wood blocks suggesting a capacity to switch to saprotrophic growth when the tree is killed. The non-pathogenic isolate had very low saprotrophic ability. Structural alterations of wood cell walls caused in the wood blocks were typical for white rot basidiomycetes. The fact that Rigidoporus microporus can switch to saprotrophic growth on dead cells of the tree led us to investigate the transcriptomic profiles of the fungus during growth on dead rubber wood. We performed RNA-Seq de novo transcriptomic assembly which produced 25, 880 annotated unigenes. The transcriptome expressed over 400 genes encoding lignocellulose enzymes. A number of glycoside hydrolases (GHs) were highly induced in rubber wood including all nine members of GH43 genes in the transcriptome. Twenty-four manganese peroxidase encoding genes were among a large number of oxidoreductases that were significantly up-regulated in rubber wood. Several genes involved in fatty acid and rubber latex degradation were expressed in the transcriptome. Several ABC transporters and hydrophobin genes were also expressed in the transcriptome. Finally, pathway enrichment analysis of genes related to energy metabolism revealed some genes including alcohol dehydrogenase with potential biotechnological applications. This is the first study on the transcriptomic analysis of R. microporus on rubber wood. The data generated should serve as a useful resource for future studies. Understanding how rubber tree is able to defend itself against invading Rigidoporus microporus was an additional research goal. The expression of defence-related genes; pathogenesis related proteins (PR1, PR3, PR5, PR8 and PR9), cell wall modification genes (PAL and expansin), signal transduction genes (ACC oxidase, AOC, MAPK) and a Myb transcription factor were studied in two clones (RRIM612 and PR107) of H. brasiliensis with different levels of susceptibility. Clone RRIM612 had a higher lesion size than clone PR107 after 5 weeks post inoculation with R. microporus. A class I chitinase (PR3) was up-regulated in RRIM612 in response to the pathogen while a class IV peroxidase (PR9) was highly up-regulated in PR107. Signal transduction genes involved in ethylene and jasmonic acid signaling as well as Phenylalanine ammonia-lyase (PAL) were up-regulated almost equally in both clones. The predicted expansin like protein was up-regulated 40 fold in RRIM612 in response to the pathogen. The results obtained demonstrate the variability in defence responses in the two clones studied and provides the first set of defence genes expression profiles of the host-pathogen interaction of the white rot disease of rubber trees. This study sheds light on the phylogeny of pathogenic Rigidoporus microporus isolates associated with the white rot disease as well as evidence showing its ability to switch to saprotrophic growth. The transcriptome of the fungus during saprotrophic growth was also de novo assembled revealing a vast number of lignocellulose degrading enzymes. Finally, this work provides an overview of potential candidate defence genes in H. brasiliensis in response to infection by R. microporus.
Source: Työväentutkimus Vuosikirja
Author: Abbot Oghenekaro
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2204289734