De Novo Analysis of Wolfiporia cocos Transcriptome to Reveal the Differentially Expressed Carbohydrate-Active Enzymes (CAZymes) Genes During the Early Stage of Sclerotial Growth

Abstract

The sclerotium of Wolfiporia cocos has been used as an edible mushroom and/or a traditional herbal medicine for centuries. W. cocos sclerotial formation is dependent on parasitism of the wood of Pinus species. Currently, the sclerotial development mechanisms of W. cocos remain largely unknown and the lack of pine resources limit the commercial production. The CAZymes (carbohydrate-active enzymes) play important roles in degradation of the plant cell wall to provide carbohydrates for fungal growth, development, and reproduction. In this study, the transcript profiles from W. cocos mycelium and 2-months-old sclerotium, the early stage of sclerotial growth, were specially analyzed using de novo sequencing technology. A total of 142,428,180 high-quality reads of mycelium and 70,594,319 high-quality reads of 2-months-old sclerotium were obtained. Additionally, differentially expressed genes from the W. cocos mycelium and 2-months-old sclerotium stages were analyzed, resulting in identification of 69 CAZymes genes which were significantly up-regulated during the early stage of sclerotial growth compared to that of in mycelium stage, and more than half of them belonged to glycosyl hydrolases (GHs) family, indicating the importance of W. cocos GHs family for degrading the pine woods. And qRT-PCR was further used to confirm the expression pattern of these up-regulated CAZymes genes. Our results will provide comprehensive CAZymes genes expression information during W. cocos sclerotial growth at the transcriptional level and will lay a foundation for functional genes studies in this fungus. In addition, our study will also facilitate the efficient use of limited pine resources, which is significant for promoting steady development of Chinese W. cocos industry.

Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms

“…Pathogens manipulate cell walls or disrupt cells walls by using plant cell wall‐degrading enzymes (PCWDEs) that are part of a larger family of carbohydrate‐active enzymes (CAZymes). These enzymes, depending upon their biology, can act upon cellulose, hemicellulose, lignin and pectin, are highly induced during pathogenesis (Hacquard et al ., ; Zhang et al ., ) and can affect the host range of a given pathogen (Baroncelli et al ., ). Given the common trait of pathogens to disrupt cell walls in this manner, plants have evolved a detection mechanism that can sense fragments of cell walls, such as hyaluronan fragments, oligogalacturonides and galacturonic acid, which, as a whole, are called ‘damage‐associated molecular patterns’ (DAMPs; Land, ).…”

The Kinome of Edible and Medicinal Fungus Wolfiporia cocos

“…Homologous sequence searches were performed with BLASTx against the S. cerevisiae database 3 and S. sclerotiorum database 4 (≥e -5 ) as described ( Hegedus et al, 2016 ; Zhang et al, 2016 ).…”

“…To identify and classify the PKs, the protein sequences from W. cocos were searched against the Kinomer v.1.0 HMM library by the using of HMMSCAN program from the HMM software suite HMMer, and the cut off value was set to 20 as previously described ( Miranda-Saavedra and Barton, 2007 ; Kosti et al, 2010 ; Wang et al, 2011 ; Zhang et al, 2016 ).…”

CAZymes-based ranking of fungi (CBRF): an interactive web database for identifying fungi with extrinsic plant biomass degrading abilities

“…Recent genomic and proteomic studies of various plant cell wall-degrading fungi were centrally focused on lignocellulolytic CAZymes their occurrence and expression (Castillo et al 2017;Geiser et al 2016;Vidal-Melgosa et al 2015;Zhang et al 2016;Zhao et al 2013). Knowing about the lignocellulolytic abilities of a microorganism prior to its experimentation will significantly benefit both the laboratory and industrial-based projects.…”

“…Similarly, we have also compared the genome-wide annotations of anaerobic fungi belonging to Neocallimastigomycota division to understand their plant cell walldegrading and biohydrogen-producing abilities. Studies focused on understanding the plant cell wall-degrading abilities of individual fungal strains were reported in the last decade (Castillo et al 2017;Geiser et al 2016;Henske et al 2017;Hüttner et al 2017;Looi et al 2017;Qin et al 2017;Vidal-Melgosa et al 2015;Zhang et al 2016).…”