Molecular analysis of capsid protein of Homalodisca coagulata Virus-1, a new leafhopper-infecting virus from the glassy-winged sharpshooter, Homalodisca coagulata

A new virus that infects and causes increased mortality in leafhoppers was isolated from the glassy-winged sharpshooter, Homalodisca coagulata (Say) (Hemiptera: Cicadellidae). The virus, named Homalodisca coagulata virus -1, HoCV-1, was associated with increased mortality of cultured 5th instar H. coagulata. To identify the presence of H. coagulata viral pathogens, cDNA expression libraries were made from adult and nymphs. Analysis using reverse transcriptase PCR demonstrated that the virus was present in midgut tissues. As the viral capsid proteins are commonly used in classification of newly discovered viruses, the capsid proteins (CP) of the virus discovered in H. coagulata was examined. The order of the polyprotein subunits of HoCV-1 capsid proteins was determined to be CP2, CP4, CP3, and CP1. The CP4/CP3 (AFGL/GKPK) cleavage boundary site was clearly identified when the sequences were aligned. The putative CP3/CP1 (ADVQ/SAFA) cleavage site and the putative CP2/CP4 (VTMQ/EQSA) cleavage site of HoCV-1, respectively, were located in the same region as that of the other viruses. After alignment, the CP3/CP1 cleavage sites and CP2/CP4 cleavage sites of the viruses analyzed fell within 50 amino acids of one another. As with the cricket paralysis virus, HoCV-1 was found to be mainly comprised of β-sandwiches in CP1-3 with a jelly roll topological motif. CP4 of HoCV-1 appeared to be mainly α-helical in structure. CP1-4 domains are most homologous to insect picorna-like virus coat proteins as was demonstrated by the results of the BLASTP and PSI-BLAST tests, and is strongly supported by the structural modeling. While sequence homology between the cricket paralysis virus and HoCV-1 was low, the global structure of the proteins was conserved. Sequence identities were analyzed by in silico comparison to known genes in the public database, NCBI. Phylogenetic analysis performed using the optimized protein alignment generated a phylogram containing 5 clades. Clade 1 consisted of Drosophila C virus, Clade 2 consisted of cricket paralysis virus, Clade 3 of Triatoma virus, Plautia stali intestine virus, Himetobi P virus, black queen cell virus, and HoCV-1. Clade 4 encompassed acute bee paralysis virus and Kashmir bee virus, and Clade 5 consisted of Rhopalosiphum padi virus. Analysis of the capsid protein of this new leafhopper virus provided significant evidence that it is related to other ssRNA insect viruses within the Family, Dicistroviridae. The HoCV-1, capsid protein sequence has been deposited in GenBank, Accession number: DQ308403

Quantification of dilatory resistance in four rice cultivars to rice blast

Due to the character of the original source materials and the nature of batch digitization, quality control issues may be present in this document. Please report any quality issues you encounter to [email protected], referencing the URI of the item.Includes bibliographical references.Dilatory resistance of two rice Cultivars, Jackson and Maybelle, to rice blast was expressed as decreases in different components of resistance. Incubation period was found to be more important in determining dilatory resistance than the other components of resistance. Lesion size and sporulation capacity were negatively correlated suggesting that increased lesion size is not necessarily indicative of decreased resistance. The negative correlation between infection frequency and lesion size further supports this idea. As sporulation capacity and infection frequency increased, incubation period decreased. These relationships imply that sporulation capacity may be more important in determining dilatory resistance than the data here suggest. P.grisea races IC-17 and IB-49 are commonly found in Texas. Component analysis found Maybelle to be more resistant to race IC-17 and Jackson to be more resistant to race IB-49 . The ability of these cultivars to withstand disease pressure in the field may therefore be influenced more by specific interactions between cultivar and pathogen population than by levels of dilatory resistance possessed by either Maybelle or Jackson

Development of a Grape Genomics Database Using IBM DB2 Content Manager Software

Diseases are a limiting factor for the growth non-native grapes in many areas of the United States. For example, Pierce’s disease limits the production of European grapes (Vitis vinifera) in most part of the southeastern United States. Disease resistance of the non-native grape could be enhanced by incorporation of the resistance traits of native American grape species such as Vitis shuttleworthii, V. aestivalis, V. riparia, and V. rotundifolia through the use of cross pollination. Alternatively, a ‘molecular breeding approach’ could be used to assist and accelerate the conventional breeding process. The recent development and availability of large number of gene sequence data makes the molecular approach more realistic than ever before. Florida A&M University (FAMU) has developed a grape genomics database using IBM DB2 Content Manager to store genetic sequences such as Expressed Sequence Tags (EST), genomic sequences, molecular markers, chromatograms, graphic information, blast hits, and functional annotations in an organized and coherent fashion. The system provides a convenient way to associate heterogeneous data sets such as genetic sequences, and various annotations with extensive search capabilities. This database system will be better served for the biological data integration and information retrieval relative to Vitis spp

Toward a Unified Genetic Map of Higher Plants, Transcending the Monocot-Dicot Divergence

Closely related (confamilial) genera often retain large chromosomal tracts in which gene order is colinear, punctuated by structural mutations such as inversions and translocations 1. To explore the possibility that conservation of gene order might extrapolate to more distantly related taxa, we first estimated an average structural mutation rate. Nine pairs of taxa, for which there exist both comparative genetic maps and plausible estimates of divergence time, showed an average of0.14 (±0.06) structural mutations per chromosome per million years of divergence (Myr; Table 1). This value is offered as a first approximation, acknowledging that refined comparative data and/or divergence estimates may impel revision.This letter is from Nature Genetics 14 (1996): 380, doi:10.1038/ng1296-380.</p