title: Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.
abstract: 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 higher 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 trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Sean P
authors.initials: SP
authors.lastname: Gordon
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Tseng
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.affiliation: Department of Bioproducts & Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Jiwei
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Xiandong
authors.initials: X
authors.lastname: Meng
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Zhiying
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Dongwan
authors.initials: D
authors.lastname: Kang
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Jason
authors.initials: J
authors.lastname: Underwood
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Melania
authors.initials: M
authors.lastname: Figueroa
authors.affiliation: Department of Bioproducts & Biosystems Engineering, University of Minnesota, Saint Paul, Minnesota, United States of America.
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Schilling
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America; School of Natural Sciences, University of California at Merced, Merced, California, United States of America.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
mesh_terms: D000363:Agaricales / Q000145:classification / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D005800:Genes, Fungal; D010802:Phylogeny; D012331:RNA, Fungal / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger