Expression profiling by high throughput sequencing
Summary
Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.
Overall design
We sequenced mRNA from 36 samples, including two brown rot and two white rot fungi, to compare the gene regulations of these two typical wood decay strategies. Each specie was used to colonize wood wafer directionally, a space for time experimental design for study wood decay successions. Then, 3 wood sections on wood wafer were sampled for RNA extraction, representing early to late decay stages, with 3 bioreplicates for each wood section for each specie.
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