Abstract
Ganoderma lucidum is a white-rot fungus best-known for its medicinal and ligninolytic activities. To discover the underlying genes responsible for these activities, we identified and characterized the natural antisense transcripts (NATs) using strand-specific (ss) RNA-seq data obtained from the mycelia, primordia and fruiting bodies. NATs were identified using a custom pipeline and then subjected to functional enrichment and differential expression analyses. A total of 1613 cis- and 244 trans- sense and antisense transcripts were identified. Mapping to GO terms and KEGG pathways revealed that NATs were frequently associated with genes of particular functional categories in particular stages. ssRT-qPCR experiments showed that the expression profiles of 30 of 50 (60%) transcripts were highly correlated with those of the RNA-seq results (r ≥ 0.9). Expression profiles of 22 of 25 (88%) pairs of NATs and STs were highly correlated (p ≤ 0.01), with 15 having r ≥ 0.8 and 4 having r ≤ -0.8. Six lignin-modifying genes and their NATs were analyzed in detail. Diverse patterns of differential expression among different stages and positive and negative correlations were observed. These results suggested that NATs were implicated in gene expression regulation in a function-group and developmental-stage specific manner through complex mechanisms.
Highlights
Ganoderma lucidum belongs to family Ganodermataceae, order Polyporales, class Agaricomycetes and phylum Basidiomycota
Based on their positions relative to the protein coding genes, long ncRNAs (lncRNAs) can be subdivided into three groups: natural antisense transcripts (NATs), long intronic non-coding RNAs (ncRNAs), and long intergenic ncRNAs7
To identify NATs of G. lucidum, we carried out strand-specific RNA
Summary
The 1630 cis-SAT pairs corresponded to 1403 STs, which were subjected to enrichment analyses for Gene Ontology (GO) terms and KEGG pathways. Two KEGG pathways, ko01200 and ko03018 were found to have been significantly enriched in both mycelia and primordia Taken together, these results suggest that NAT might play important roles in a developmental-stage specific manner. To verify the ssRNA-seq results, we applied ssRT-qPCR technology to quantify the expression levels of a selected set of NATs and their corresponding STs. The genes chosen for this comparison are those members of the CYP450 superfamily and those participate in the lignin degradation pathway (Table S9). Category ID GO:0055085 GO:0004497 GO:0005506 GO:0009055 GO:0020037 GO:0055114 GO:0006810 GO:0043169 GO:0016491 ko03030 ko00500 ko03410 ko00627
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