Transcriptomics,Multiomics

Dataset Information

3

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [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. Small RNA sequence data from Phytophthora infestans-infected potato leaf tissue and P. infestans mycelium tissue. Three infection stage time-points. Two P. infestans lines: 88089 (wild-type) and PiDcl1 (transformant PiDcl1 knock-down). No replicates. Total number of samples: 8.

OTHER RELATED OMICS DATASETS IN: PRJNA267207PRJNA264780PRJNA267210

ORGANISM(S): Phytophthora infestans  

SUBMITTER: Johan Fogelqvist   Christina Dixelius  Stephen C Whisson  Sultana N Jahan  Anna Åsman  Anna K Åsman  Pádraic Corcoran  Anna O Avrova  Ramesh R Vetukuri 

PROVIDER: E-GEOD-63292 | ArrayExpress | 2014-12-12

SECONDARY ACCESSION(S): GSE63292SRP049812PRJNA267210

REPOSITORIES: GEO, ArrayExpress, ENA

Dataset's files

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E-GEOD-63292.additional.1.zip Other
E-GEOD-63292.idf.txt Idf
E-GEOD-63292.sdrf.txt Txt
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Publications

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection.

Åsman Anna K M AK   Vetukuri Ramesh R RR   Jahan Sultana N SN   Fogelqvist Johan J   Corcoran Pádraic P   Avrova Anna O AO   Whisson Stephen C SC   Dixelius Christina C  

BMC microbiology 20141210


<h4>Background</h4>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.<h4>Results</h4>To identify additional classes of sRNAs in oomycetes, we mapped  ...[more]

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