title: Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.
abstract: In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America ; Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.
authors.forename: Noah
authors.initials: N
authors.lastname: Fahlgren
authors.forename: Stephanie R
authors.initials: SR
authors.lastname: Bollmann
authors.forename: Kristin D
authors.initials: KD
authors.lastname: Kasschau
authors.forename: Josh T
authors.initials: JT
authors.lastname: Cuperus
authors.forename: Caroline M
authors.initials: CM
authors.lastname: Press
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Sullivan
authors.forename: Elisabeth J
authors.initials: EJ
authors.lastname: Chapman
authors.forename: J Steen
authors.initials: JS
authors.lastname: Hoyer
authors.forename: Kerrigan B
authors.initials: KB
authors.lastname: Gilbert
authors.forename: Niklaus J
authors.initials: NJ
authors.lastname: Grünwald
authors.forename: James C
authors.initials: JC
authors.lastname: Carrington
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D004251:DNA Transposable Elements; D047150:Eosinophil Cationic Protein / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D005353:Fibronectins / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D056426:Genetic Loci; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D010838:Phytophthora / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010935:Plant Diseases; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
chemical_list: D004251:DNA Transposable Elements; D005353:Fibronectins; D035683:MicroRNAs; D034741:RNA, Small Interfering; D047150:Eosinophil Cationic Protein