title: Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae.
abstract: Small RNAs are well described in higher eukaryotes such as mammals and plants; however, knowledge in simple eukaryotes such as filamentous fungi is limited. In this study, we discovered and characterized methylguanosine-capped and polyadenylated small RNAs (CPA-sRNAs) by using differential RNA selection, full-length cDNA cloning and 454 transcriptome sequencing of the rice blast fungus Magnaporthe oryzae. This fungus causes blast, a devastating disease on rice, the principle food staple for over half the world's population. CPA-sRNAs mapped primarily to the transcription initiation and termination sites of protein-coding genes and were positively correlated with gene expression, particularly for highly expressed genes including those encoding ribosomal proteins. Numerous CPA-sRNAs also mapped to rRNAs, tRNAs, snRNAs, transposable elements and intergenic regions. Many other 454 sequence reads could not be mapped to the genome; however, inspection revealed evidence for non-template additions and chimeric sequences. CPA-sRNAs were independently confirmed using a high affinity variant of eIF-4E to capture 5'-methylguanosine-capped RNA followed by 3'-RACE sequencing. These results expand the repertoire of small RNAs in filamentous fungi.
authors.affiliation: Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27606, USA.
authors.forename: Malali
authors.initials: M
authors.lastname: Gowda
authors.forename: Cristiano C
authors.initials: CC
authors.lastname: Nunes
authors.forename: Joshua
authors.initials: J
authors.lastname: Sailsbery
authors.forename: Minfeng
authors.initials: M
authors.lastname: Xue
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.forename: Cassie A
authors.initials: CA
authors.lastname: Nelson
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Brown
authors.forename: Yeonyee
authors.initials: Y
authors.lastname: Oh
authors.forename: Shaowu
authors.initials: S
authors.lastname: Meng
authors.forename: Thomas
authors.initials: T
authors.lastname: Mitchell
authors.forename: Curt H
authors.initials: CH
authors.lastname: Hagedorn
authors.forename: Ralph A
authors.initials: RA
authors.lastname: Dean
mesh_terms: D001483:Base Sequence; D005656:Fungal Proteins / Q000235:genetics; D016681:Genome, Fungal; D006151:Guanosine / Q000031:analogs & derivatives* / Q000032:analysis; D020082:Magnaporthe / Q000235:genetics*; D008969:Molecular Sequence Data; D011061:Poly A / Q000032:analysis*; D012315:RNA Caps / Q000737:chemistry*; D012318:RNA Polymerase I / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: C116616:8-methylguanosine; D005656:Fungal Proteins; D012315:RNA Caps; D012331:RNA, Fungal; D058727:RNA, Small Untranslated; D006151:Guanosine; D011061:Poly A; D012319:RNA Polymerase II; D012318:RNA Polymerase I