| Title |
Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans
|
|---|---|
| Published in |
PLOS ONE, December 2012
|
| DOI | 10.1371/journal.pone.0051399 |
| Pubmed ID | |
| Authors |
Ramesh R. Vetukuri, Anna K. M. Åsman, Christian Tellgren-Roth, Sultana N. Jahan, Johan Reimegård, Johan Fogelqvist, Eugene Savenkov, Fredrik Söderbom, Anna O. Avrova, Stephen C. Whisson, Christina Dixelius |
| 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. |
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Canada | 2 | 18% |
| France | 2 | 18% |
| United Kingdom | 2 | 18% |
| Belgium | 1 | 9% |
| Egypt | 1 | 9% |
| Unknown | 3 | 27% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 5 | 45% |
| Scientists | 5 | 45% |
| Science communicators (journalists, bloggers, editors) | 1 | 9% |
Mendeley readers
The data shown below were compiled from readership statistics for 115 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 2 | 2% |
| India | 2 | 2% |
| Australia | 1 | <1% |
| Brazil | 1 | <1% |
| United States | 1 | <1% |
| Unknown | 108 | 94% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 35 | 30% |
| Student > Ph. D. Student | 22 | 19% |
| Student > Master | 11 | 10% |
| Professor > Associate Professor | 8 | 7% |
| Student > Bachelor | 6 | 5% |
| Other | 21 | 18% |
| Unknown | 12 | 10% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 69 | 60% |
| Biochemistry, Genetics and Molecular Biology | 23 | 20% |
| Psychology | 1 | <1% |
| Physics and Astronomy | 1 | <1% |
| Earth and Planetary Sciences | 1 | <1% |
| Other | 3 | 3% |
| Unknown | 17 | 15% |