title: Comparative analysis of virus-derived small RNAs within cassava (Manihot esculenta Crantz) infected with cassava brown streak viruses.
abstract: Infection of plant cells by viral pathogens triggers RNA silencing, an innate antiviral defense mechanism. In response to infection, small RNAs (sRNAs) are produced that associate with Argonaute (AGO)-containing silencing complexes which act to inactivate viral genomes by posttranscriptional gene silencing (PTGS). Deep sequencing was used to compare virus-derived small RNAs (vsRNAs) in cassava genotypes NASE 3, TME 204 and 60444 infected with the positive sense single-stranded RNA (+ssRNA) viruses cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), the causal agents of cassava brown streak disease (CBSD). An abundance of 21-24nt vsRNAs was detected and mapped, covering the entire CBSV and UCBSV genomes. The 21nt vsRNAs were most predominant, followed by the 22 nt class with a slight bias toward sense compared to antisense polarity, and a bias for adenine and uracil bases present at the 5'-terminus. Distribution and frequency of vsRNAs differed between cassava genotypes and viral genomes. In susceptible genotypes TME 204 and 60444, CBSV-derived sRNAs were seen in greater abundance than UCBSV-derived sRNAs. NASE 3, known to be resistant to UCBSV, accumulated negligible UCBSV-derived sRNAs but high populations of CBSV-derived sRNAs. Transcript levels of cassava homologues of AGO2, DCL2 and DCL4, which are central to the gene-silencing complex, were found to be differentially regulated in CBSV- and UCBSV-infected plants across genotypes, suggesting these proteins play a role in antiviral defense. Irrespective of genotype or viral pathogen, maximum populations of vsRNAs mapped to the cytoplasmic inclusion, P1 and P3 protein-encoding regions. Our results indicate disparity between CBSV and UCBSV host-virus interaction mechanisms, and provide insight into the role of virus-induced gene silencing as a mechanism of resistance to CBSD.
authors.affiliation: National Crops Resources Research Institute, Namulonge, P.O Box 7084, Kampala, Uganda; Institute for International Crop Improvement, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, P.O Wits 2050, Johannesburg, South Africa.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Ogwok
authors.affiliation: Institute for International Crop Improvement, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ilyas
authors.affiliation: National Crops Resources Research Institute, Namulonge, P.O Box 7084, Kampala, Uganda.
authors.forename: Titus
authors.initials: T
authors.lastname: Alicai
authors.affiliation: School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, P.O Wits 2050, Johannesburg, South Africa.
authors.forename: Marie E C
authors.initials: ME
authors.lastname: Rey
authors.affiliation: Institute for International Crop Improvement, Donald Danforth Plant Science Center, St. Louis, MO 63132, USA. Electronic address: ntaylor@danforthcenter.org.
authors.forename: Nigel J
authors.initials: NJ
authors.lastname: Taylor
mesh_terms: D020868:Gene Silencing; D054884:Host-Pathogen Interactions; D002365:Manihot / Q000276:immunology / Q000821:virology*; D010935:Plant Diseases / Q000821:virology*; D019176:Potyviridae / Q000235:genetics* / Q000254:growth & development*; D058727:RNA, Small Untranslated / Q000032:analysis*; D012367:RNA, Viral / Q000032:analysis*
chemical_list: D058727:RNA, Small Untranslated; D012367:RNA, Viral
keywords: Deep sequencing; cassava; cassava brown streak disease; virus-derived small RNA
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