Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae.
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.
Gowda
Malali
M
Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27606, USA.
Nunes
Cristiano C
CC
Sailsbery
Joshua
J
Xue
Minfeng
M
Chen
Feng
F
Nelson
Cassie A
CA
Brown
Douglas E
DE
Oh
Yeonyee
Y
Meng
Shaowu
S
Mitchell
Thomas
T
Hagedorn
Curt H
CH
Dean
Ralph A
RA
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
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