Abstract
This study investigates the evolution of truffle-like fruiting bodies from a classic mushroom fruiting body. It investigates both protein coding genes and non-coding RNAs. Noncoding RNAs have not been studied systematically in any mushroom and few ncRNA have been identified on reference genomes.
A new, more complete assembly of Coprinopsis cinerea A43mut B43mut pab1-1 #326, original and publicly available RNA-Seq data, as well as RNA structure prediction methodologies were employed to identify putative novel and known ncRNAs. Reassingment of previously identified “hypothetical” proteins was also performed. To further characterise putative ncRNAs as likely ncRNA, coding potential analysis and InterProScan for functional domain identification was performed. These findings revealed 8720 novel ncRNAs of which 3537 had been incorrectly identified in the reference annotation, with 6255 ncRNA showing measurable expression during development. Furthermore, differential expression analysis identified 2195 ncRNAs and 7217 mRNAs exhibiting differential expression between developmental stages.
Through clustering and network analysis, related genes were grouped into clusters with common expression. I discovered ncRNAs demonstrated more connections or edges than mRNAs, implying a potentially central role in gene regulatory networks. Importantly, a number of potential cis-regulatory ncRNA-mRNA pairs were identified based on their cluster affiliation and proximity using gcen for network construction and module identification. Overall 9926 mRNA with at least one potential regulatory ncRNA were identified. Analysis of GO terms and Pfam identifiers of regulated mRNA genes identifies a wide range of potential candidate ncRNA involved in the development of fruiting bodies.
Collectively, these findings indicate the crucial role of ncRNAs in the morphogenesis of fungal fruiting bodies and provide a promising avenue for future research on their role in development of complex fungal fruiting body forms.