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Project description:The Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV) can be propagated using H. zea insect cell cultures, for use as a biopesticide against Heliothine agricultural pests.This study sequenced, assembled and functionally annotated 29,586 transcript sequences from cultured H. zea cells using Illumina 100 bps and paired-end transcriptome sequencing (RNA-seq). From these sequences, a genome-scale microarray platform was constructed and validated for effective expression analysis of H. zea genes. This array also included probes for all HaSNPV genes, thereby allowing virus and host gene changes to be monitored simultaneously. A 4x180,000 SurePrint Agilent expression array (Agilent, Santa Clara, CA) was employed so that a high number of probes can be included to test all 29,586 assembled H. zea sequences and to eventually select a best probe for each transcript. Two biological replicates for uninfected H. zea cells and two other biological replicates for infected samples at 18 hours post infection were analyzed. Six Agilent 60-mer oligonucleotide probes were designed by eArray (Agilent) for each transcript, in which each orientation had three probes randomly distributed across the sequences. Probes that had potential cross-hybridization (Xhyb) were removed. The final probe set for H. zea sequences included 153,583 probes. In addition, probes for all 135 H.armigera single-capsid nucleopolyhedrovirus (HaSNPV) genes were added to investigate host-virus interaction in culture.
2012-03-01 | E-GEOD-34418 | biostudies-arrayexpress
Project description:Grapevine line pattern virus (GLPV) was described 30 years ago from Hungary, and in the lack of its sequence until now no additional information about its presence was reported. However High-Throughput Sequencing (HTS) applied on dsRNAs extracts recovered from a grapevine plant (accession Baco22A) infected with GLPV Grapevine line pattern virus (GLPV) allowed us to sequence it with different High-Throughput Sequencing (HTS) methods andthe assembleing of the full genome sequence of this virus. The availability of the sequence allowed us to validate the presence of the virus bot with RT-PCR and with Northern blot hybridization. These methods were also used to test its graft and seed transmission. In accordance as it was originally suggested its genome was found to comprise three RNA segments.Its RNA1 (3.160 bp), RNA2 (2.493 bp) and RNA3 (2.529 bp), encode four proteins, denoted 1a (Methyltransferase, helicase), 2a (RNA-dependent RNA Polymerase), 3a (Movement protein, MP) and 3b (Coat protein, CP). GLPV showed the highest amino acid identity (92%–99%) with all domains of Hop yellow virus (HYV), which is a tentative member of the genus Anulavirus of the family Bromoviridae. The phylogenetic trees constructed based on the amino acid sequences of 2a and 3b also confirmed the belongingness of GLPV to the genus Anulavirus, allocating it in one cluster together with the anulaviruses, and close to HYV. The very high sequence identity found between GLPV and HYV leaves no doubt that both are two isolates of the same viral species.
2020-06-03 | GSE148246 | GEO