De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood

Abstract

BackgroundThe basidiomycete Rigidoporus microporus is a fungus that causes the white rot disease of the tropical rubber tree, Hevea brasiliensis, the major source of commercial natural rubber. Besides its lifestyle as a pathogen, the fungus is known to switch to saprotrophic growth on wood with the ability to degrade both lignin and cellulose. There is almost no genomic or transcriptomic information on the saprotrophic abilities of this fungus. In this study, we present the fungal transcriptomic profiles during saprotrophic growth on rubber wood.ResultsA total of 266.6 million RNA-Seq reads were generated from six libraries of the fungus growing either on rubber wood or without wood. De novo assembly produced 34, 518 unigenes with an average length of 2179 bp. Annotation of unigenes using public databases; GenBank, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups (COG) and Gene Ontology (GO) produced 25, 880 annotated unigenes. Transcriptomic profiling analysis revealed that the fungus expressed over 300 genes encoding lignocellulolytic enzymes. Among these, 175 genes were up-regulated in rubber wood. These include three members of the glycoside hydrolase family 43, as well as various glycosyl transferases, carbohydrate esterases and polysaccharide lyases. A large number of oxidoreductases which includes nine manganese peroxidases were also significantly up-regulated in rubber wood. Several genes involved in fatty acid metabolism and degradation as well as natural rubber degradation were expressed in the transcriptome. Four genes (acyl-CoA synthetase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA acetyltransferase) potentially involved in rubber latex degradation pathway were also induced. A number of ATP binding cassette (ABC) transporters and hydrophobin genes were significantly expressed in the transcriptome during saprotrophic growth. Some genes related to energy metabolism were also induced.ConclusionsThe analysed data gives an insight into the activation of lignocellulose breakdown machinery of R. microporus. This study also revealed genes with relevance in antibiotic metabolism (e.g. cephalosporin esterase) as well as those with potential applications in fatty acid degradation. This is the first study on the transcriptomic analysis of R. microporus on rubber wood and should serve as a pioneering resource for future studies of the fungus at the genomic or transcriptomic level.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2574-9) contains supplementary material, which is available to authorized users.

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

“…The genome size of R. microporus is within the range reported for other members of Hymenochaetales. Using diverse www.nature.com/scientificreports www.nature.com/scientificreports/ gene prediction methods, which included the use of previously generated RNA-seq data 10 , we predicted 10,917 protein-coding genes. The mitochondrial genome of R. microporus contains 27 predicted protein-coding genes ( Supplementary Table 3) and 24 tRNA genes ( Supplementary Table 4).…”

De novo transcriptomic assembly and mRNA expression patterns of Botryosphaeria dothidea infection with mycoviruses chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1)

“…To better survey the biological behavior of defense response, it is necessary to understand the functional distribution of these DEGs in B. dothidea following mycovirus infection based on the transcriptome and bioinformatics analysis [ 44 – 47 ]. Through the enriched GO terms analysis, it is also revealed that in biological processes, DEGs mainly distributed to metabolism.…”

Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species

“…and polysaccharide lyase (PL) cocktails [ 3 , 27 ]. Fungi from multiple white-rot and brown-rot clades have been used to study the wood-decay associated gene expression [ 28 , 29 , 30 , 31 , 32 ]. These studies highlighted substrate and species-specific responses, sequential activation of degradative enzymes, along with lifestyle-driven differences among species highlighting the ambiguity of extant decay-type classification.…”