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.
Highlights
Small noncoding RNAs of 20–40 nucleotides have emerged as key players in both transcriptional and posttranscriptional gene regulation in an array of organisms [1]
P. infestans Produces at Least Three Size Classes of small RNA molecules (sRNA) Molecules
Of the sRNAs not derived from tRNAs and rRNAs, 6.6–15.6% mapped to the dataset of the entire genome sequence, and a further 6.2– 17.0% mapped to the dataset of unplaced sequence reads from the P. infestans genome database (Table S1; Figure S2A, B)
Summary
Small noncoding RNAs (sRNAs) of 20–40 nucleotides (nt) have emerged as key players in both transcriptional and posttranscriptional gene regulation in an array of organisms [1]. They play important roles in genome stability, chromatin organization, and virus resistance [2]. Known as water molds, are fungus-like heterotrophs which are ubiquitous in marine, freshwater and terrestrial environments [5]. This group of organisms belongs to the lineage of biflagellate Stramenopiles within the kingdom Chromista [6,7]. Oomycetes are distantly related to the Apicomplexa, such as Plasmodium and Toxoplasma parasites [9]
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