Transcriptional analysis of South African cassava mosaic virus-infected susceptible and tolerant landraces of cassava highlights differences in resistance, basal defense and cell wall associated genes during infection

Cassava mosaic disease is caused by several distinct geminivirus species, including South African cassava mosaic virus-[South Africa:99] (SACMV). To date, there is limited gene regulation information on viral stress responses in cassava, and global transcriptome profiling in SACMV-infected cassava r...

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Bibliographic Details
Published in:BMC genomics 2014-11, Vol.15 (1), p.1006-1006, Article 1006
Main Authors: Allie, Farhahna, Pierce, Erica J, Okoniewski, Michal J, Rey, Chrissie
Format: Article
Language:English
Subjects:
Analysis
Arabidopsis - virology
Cassava
Cell Wall - genetics
Defense
Deoxyribonucleic acid
Disease Resistance - genetics
DNA
DNA binding proteins
DNA methylation
Down-Regulation - genetics
Geminiviridae - pathogenicity
Geminiviridae - physiology
Geminivirus
Gene Expression Profiling
Gene Expression Regulation, Plant
Gene Ontology
Genes
Genes, Plant
Genetic aspects
Genetic research
Genomic libraries
Genomics
Health aspects
Infections
Manihot - genetics
Manihot - virology
Manihot esculenta
Metabolic Networks and Pathways - genetics
Molecular Sequence Annotation
Mosaic Viruses - pathogenicity
Mosaic Viruses - physiology
Plant Diseases - genetics
Plant Diseases - virology
Plant Leaves - virology
Plant Proteins - genetics
Plant Proteins - metabolism
Proteins
Pulp & paper industry
Real-Time Polymerase Chain Reaction
Reproducibility of Results
RNA, Messenger - genetics
RNA, Messenger - metabolism
Signal Transduction - genetics
South Africa
Transcriptome - genetics
Viruses
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Summary:Cassava mosaic disease is caused by several distinct geminivirus species, including South African cassava mosaic virus-[South Africa:99] (SACMV). To date, there is limited gene regulation information on viral stress responses in cassava, and global transcriptome profiling in SACMV-infected cassava represents an important step towards understanding natural host responses to plant geminiviruses. A RNA-seq time course (12, 32 and 67 dpi) study, monitoring gene expression in SACMV-challenged susceptible (T200) and tolerant (TME3) cassava landraces, was performed using the Applied Biosystems (ABI) SOLiD next-generation sequencing platform. The multiplexed paired end sequencing run produced a total of 523 MB and 693 MB of paired-end reads for SACMV-infected susceptible and tolerant cDNA libraries, respectively. Of these, approximately 50.7% of the T200 reads and 55.06% of TME3 reads mapped to the cassava reference genome available in phytozome. Using a log2 fold cut-off (p
ISSN:1471-2164
1471-2164
DOI:10.1186/1471-2164-15-1006