Seasonal Phenology of Amphorophora agathonica (Hemiptera: Aphididae) and Spread of Viruses in Red Raspberry in Washington

Amphorophora agathonica (Hottes) is the primary vector of aphid-transmitted viruses in red raspberry in the Pacific Northwest region of the United States. To better understand the biology of the aphid, we estimated the lower developmental threshold and studied the seasonal activity of A. agathonica in commercial fields in northern Washington state. In addition, we monitored the spread of raspberry viruses (raspberry latent virus and raspberry leaf mottle virus, RLMV) to determine how rapidly fields became infected and whether there was a relationship between aphid presence and infection. The lower developmental threshold of A. agathonica was estimated to be 2.7°C. In the field, apterous and alate aphid populations began rapidly increasing at ≈800 growing degree-days and peaked at 1,050 growing degree-days. RLMV spread rapidly, with 30–60% of plants in four different commercial fields testing positive after three growing seasons. There was no discernible relationship between the presence or abundance of aphids based on 10 leaves sampled per plant location, and the odds of that plant becoming infected with RLMV.This is the publisher’s final pdf. The published article is copyrighted by the Entomological Society of America and can be found at: http://www.bioone.org/loi/enveKeywords: Reoviridae, Closteroviridae, RpLV, RLMV, Raspberry aphi

The Genetics and Genomics of Virus Resistance in Maize

Viruses cause significant diseases on maize worldwide. Intensive agronomic practices, changes in vector distribution, and the introduction of vectors and viruses into new areas can result in emerging disease problems. Because deployment of resistant hybrids and cultivars is considered to be both economically viable and environmentally sustainable, genes and quantitative trait loci for most economically important virus diseases have been identified. Examination of multiple studies indicates the importance of regions of maize chromosomes 2, 3, 6, and 10 in virus resistance. An understanding of the molecular basis of virus resistance in maize is beginning to emerge, and two genes conferring resistance to sugarcane mosaic virus, Scmv1 and Scmv2, have been cloned and characterized. Recent studies provide hints of other pathways and genes critical to virus resistance in maize, but further work is required to determine the roles of these in virus susceptibility and resistance. This research will be facilitated by rapidly advancing technologies for functional analysis of genes in maize

Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya.

The complete genome of a new rhabdovirus infecting papaya (Carica papaya L.) in Ecuador, named papaya virus E, was sequenced and characterized. The negative-sense single-stranded RNA genome consists of 13,469 nucleotides with six canonical open reading frames (ORFs) and two accessory short ORFs predicted between ORFs corresponding to P3 (movement protein) and M (matrix protein). Phylogenetic analyses using amino acid sequences from the nucleocapsid, glycoprotein and polymerase, grouped the virus with members of the genus Cytorhabdovirus, with rice stripe mosaic virus, yerba mate chlorosis-associated virus and Colocasia bobone disease-associated virus as closest relatives. The 3' leader and 5' trailer sequences were 144 and 167 nt long, respectively, containing partially complementary motifs. The motif 3'-AUUCUUUUUG-5', conserved across rhabdoviruses, was identified in all but one intergenic regions; whereas the motif 3'-ACAAAAACACA-5' was found in three intergenic junctions. This is the first complete genome sequence of a cytorhabdovirus infecting papaya. The virus was prevalent in commercial plantings of Los Ríos, the most important papaya producing province of Ecuador. Recently, the genome sequence of bean-associated cytorhabdovirus was reported. The genome is 97% identical to that of papaya virus E, indicating that both should be considered strains of the same virus

Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently "Orphan" Viral Proteins

The genome sequences of new viruses often contain many “orphan” or “taxon-specific” proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as “genus specific” by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virions