title: Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans.
abstract: Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19-40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs.
authors.affiliation: Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden. Ramesh.Vetukuri@slu.se
authors.forename: Ramesh R
authors.initials: RR
authors.lastname: Vetukuri
authors.forename: Anna K M
authors.initials: AK
authors.lastname: Åsman
authors.forename: Christian
authors.initials: C
authors.lastname: Tellgren-Roth
authors.forename: Sultana N
authors.initials: SN
authors.lastname: Jahan
authors.forename: Johan
authors.initials: J
authors.lastname: Reimegård
authors.forename: Johan
authors.initials: J
authors.lastname: Fogelqvist
authors.forename: Eugene
authors.initials: E
authors.lastname: Savenkov
authors.forename: Fredrik
authors.initials: F
authors.lastname: Söderbom
authors.forename: Anna O
authors.initials: AO
authors.lastname: Avrova
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Whisson
authors.forename: Christina
authors.initials: C
authors.lastname: Dixelius
mesh_terms: D015152:Blotting, Northern; D002874:Chromosome Mapping / Q000379:methods; D004251:DNA Transposable Elements; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D018551:Solanum lycopersicum; D035683:MicroRNAs / Q000378:metabolism; D008954:Models, Biological; D008957:Models, Genetic; D009868:Oomycetes / Q000378:metabolism*; D055750:Phytophthora infestans / Q000378:metabolism*; D010935:Plant Diseases / Q000382:microbiology; D012313:RNA / Q000235:genetics*; D034622:RNA Interference; D058727:RNA, Small Untranslated / Q000235:genetics*; D011198:Solanum tuberosum; D020079:Terminal Repeat Sequences
chemical_list: D004251:DNA Transposable Elements; D035683:MicroRNAs; D058727:RNA, Small Untranslated; D012313:RNA