Abstract
Shiraia bambusicola is a species of the monotypic genus Shiraia in the phylum Ascomycota. In China, it is known for its pharmacological properties that are used to treat rheumatic arthritis, sciatica, pertussis, tracheitis and so forth. Its major medicinal active metabolite is hypocrellin A, which exhibits excellent antiviral and antitumor properties. However, the genes involved in the hypocrellin A anabolic pathways were still unknown due to the lack of genomic information for this species. To investigate putative genes that are involved in the biosynthesis of hypocrellin A and determine the pathway, we performed transcriptome sequencing for Shiraia bambusicola S4201-W and the mutant S4201-D1 for the first time. S4201-W has excellent hypocrellin A production, while the mutant S4201-D1 does not. Then, we obtained 38,056,034 and 39,086,896 clean reads from S4201-W and S4201-D1, respectively. In all, 17,923 unigenes were de novo assembled, and the N50 length was 1970 bp. Based on the negative binomial distribution test, 716 unigenes were found to be upregulated, and 188 genes were downregulated in S4201-D1, compared with S4201-W. We have found seven unigenes involved in the biosynthesis of hypocrellin A and proposed a putative hypocrellin A biosynthetic pathway. These data will provide a valuable resource and theoretical basis for future molecular studies of hypocrellin A, help identify the genes involved in the biosynthesis of hypocrellin A and help facilitate functional studies for enhancing hypocrellin A production.
Highlights
Shiraia bambusicola is a species of the monotypic genus Shiraia in the phylum Ascomycota
Carotenoids are one of the formation of binding sites for repressor proteins in the upstream region of the transcription start sites; (4) we found that there are no significant differences in expression of transcription factors between the wild type and the mutant, and the cause of the lack of Hypocrellin A (HA) biosynthesis may not be the change in numbers of transcription factors
We selected six unigenes involved in HA biosynthesis and four Differentially expressed genes (DEGs) randomly chosen through quantitative real time PCR to validate the changes in gene expression identified by RNA-Seq
Summary
Shiraia bambusicola is a species of the monotypic genus Shiraia in the phylum Ascomycota. We can use the working model of cercosporin biosynthetic pathway to study the biosynthesis of HA. The first gene putatively identified in the pathway was cercosporin facilitator protein (CFP), which has high homology with MFS drug resistance transporter proteins and was found to be required for exportation of cercosporin from the mycelium of Cercospora kikuchii [18]. To investigate putative genes involved in the biosynthesis of HA and propose a putative biosynthetic pathway, firstly we screened a hypocrellin-producing strain S4201-W, which was isolated from the fruiting bodies of the Shiraia bambusicola P. The Illumina HiSeqTM 2500 platform was used to sequence the transcriptome of Shiraia bambusicola to study its molecular genetics and HA biosynthesis. This study will provide an important resource for gene discovery and increase HA production in Shiraia bambusicola through further genetic manipulation
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