Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.
Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.
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DOI：
10.1371/journal.pone.0132628
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Wang Z
中科院分区：
文献类型：
--
作者：
Gordon SP;Tseng E;Salamov A;Zhang J;Meng X;Zhao Z;Kang D;Underwood J;Grigoriev IV;Figueroa M;Schilling JS;Chen F;Wang Z
原核生物基因组中的基因通常排列成簇并共转录成多顺反子RNA。在一些高等真核生物中也报道了多顺反子RNA的孤立例子，但它们的存在通常被认为是罕见的。在这里，我们开发了一种长读段测序策略，以确定多顺反子转录在几个蘑菇形成真菌物种，包括褶皱拟盘孢，黄孢原毛革菌，变色栓菌，密粘褶菌。我们发现在这些伞菌中多顺反子转录的全基因组流行，涉及高达8%的转录基因。与原核生物中的多顺反子mRNA不同，这些共转录基因也独立转录。我们发现，多顺反子转录可能会干扰下游串联基因的表达。进一步的比较基因组分析表明，多顺反子转录是保守的范围广泛的蘑菇形成真菌。总之，我们的研究首次揭示了多顺反子转录在高等真菌系统发育范围内的基因组普遍性。此外，我们系统地表明，我们的长读测序方法和组合的生物信息学管道是精确表征复杂转录组的通用强大工具，可以识别通过短读组装无法恢复的mRNA亚型。
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.