title: Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection.
abstract: BACKGROUND
  The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host.
  
  
  RESULTS
  To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line.
  
  
  CONCLUSIONS
  Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans.
authors.affiliation: Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Anna.Asman@slu.se.
authors.forename: Anna K M
authors.initials: AK
authors.lastname: Åsman
authors.affiliation: Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Ramesh.Vetukuri@slu.se.
authors.forename: Ramesh R
authors.initials: RR
authors.lastname: Vetukuri
authors.affiliation: Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Sultana.Jahan@slu.se.
authors.forename: Sultana N
authors.initials: SN
authors.lastname: Jahan
authors.affiliation: Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Johan.Fogelqvist@slu.se.
authors.forename: Johan
authors.initials: J
authors.lastname: Fogelqvist
authors.affiliation: Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. padraiccorcoran1@gmail.com.|Current affiliation: Department of Evolutionary Biology, Uppsala University, SE-75236, Uppsala, Sweden. padraiccorcoran1@gmail.com.
authors.forename: Pádraic
authors.initials: P
authors.lastname: Corcoran
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Anna.Avrova@hutton.ac.uk.
authors.forename: Anna O
authors.initials: AO
authors.lastname: Avrova
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK. Steve.Whisson@hutton.ac.uk.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Whisson
authors.affiliation: Department of Plant Biology, Uppsala BioCenter, Linnéan Centre for Plant Biology, Swedish University of Agricultural Sciences, PO. Box 7080, SE-75007, Uppsala, Sweden. Christina.Dixelius@slu.se.
authors.forename: Christina
authors.initials: C
authors.lastname: Dixelius
mesh_terms: D015152:Blotting, Northern; D015966:Gene Expression Regulation, Fungal; D020868:Gene Silencing; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D008018:Life Cycle Stages; D055750:Phytophthora infestans / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D010935:Plant Diseases / Q000382:microbiology*; D012331:RNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011198:Solanum tuberosum / Q000382:microbiology*
chemical_list: D012331:RNA, Fungal; D012343:RNA, Transfer