PT  - JOURNAL ARTICLE
AU  - Gordon, Sean P.
AU  - Tseng, Elizabeth
AU  - Salamov, Asaf
AU  - Zhang, Jiwei
AU  - Meng, Xiandong
AU  - Zhao, Zhiying
AU  - Kang, Dongwan
AU  - Underwood, Jason
AU  - Grigoriev, Igor V.
AU  - Figueroa, Melania
AU  - Schilling, Jonathan S.
AU  - Chen, Feng
AU  - Wang, Zhong
TI  - Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing
AID  - 10.1101/012542
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 012542
4099  - http://biorxiv.org/content/early/2014/12/11/012542.short
4100  - http://biorxiv.org/content/early/2014/12/11/012542.full
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.