RT Journal Article
SR Electronic
T1 Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 012542
DO 10.1101/012542
A1 Sean P. Gordon
A1 Elizabeth Tseng
A1 Asaf Salamov
A1 Jiwei Zhang
A1 Xiandong Meng
A1 Zhiying Zhao
A1 Dongwan Kang
A1 Jason Underwood
A1 Igor V. Grigoriev
A1 Melania Figueroa
A1 Jonathan S. Schilling
A1 Feng Chen
A1 Zhong Wang
YR 2014
UL http://biorxiv.org/content/early/2014/12/11/012542.abstract
AB Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor and Gloeophyllum trabeum1. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, and it involves up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed, and upstream transcription may interfere downstream transcription. Further comparative genomic analysis indicates that polycistronic transcription is likely a feature unique to these fungi. In addition, we also systematically demonstrated that short-read assembly is insufficient for mRNA isoform discovery, especially for isoform-rich loci. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a subset of fungi. Futhermore, our long-read sequencing approach combined with bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes.