Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum

PLoS One. 2014 Jun 16;9(6):e99442. doi: 10.1371/journal.pone.0099442. eCollection 2014.

Abstract

Ganoderma lucidum is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in G. lucidum genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA) in G. lucidum systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from G. lucidum samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes) revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3' RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8) and 5 are negatively correlated (r<-0.8). The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in G. lucidum.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping
  • Chromosomes, Fungal / genetics
  • Computational Biology / methods
  • Fungal Proteins / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal / genetics*
  • Genes, Fungal
  • Genome, Fungal*
  • Lignin / metabolism
  • Mycelium / physiology
  • Polymerase Chain Reaction / methods
  • RNA, Fungal / genetics*
  • RNA, Fungal / isolation & purification
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / isolation & purification
  • Reishi / genetics*
  • Reishi / growth & development
  • Reishi / metabolism
  • Sequence Analysis, RNA
  • Transcription, Genetic
  • Triterpenes / metabolism

Substances

  • Fungal Proteins
  • RNA, Fungal
  • RNA, Long Noncoding
  • Triterpenes
  • Lignin

Grants and funding

This study was supported by the National Science Foundation of China granted to C. Liu (Grant No. 81373912), a start fund from the Chinese Academy of Medical Science (Grant No. 431118), the Basic Scientific Research Operation Grants for State-Level Public Welfare Scientific Research Initiatives (Grant No. YZ-12-04), a research grant for returned Overseas Chinese Scholars, and Ministry of Human Resources (Grant No. 431207). This study was also supported by the National Science Foundation of China (Grant No. 81274015) granted to B. Wu and the Program for Changjiang Scholars and Innovative Research Team in the University from Ministry of Education of China (Grant No. IRT1150). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.