Development of High Throughput Transcriptome Sequences
Sustainable Perennial Crops
2013 Annual Report
1a.Objectives (from AD-416):
The objective of this agreement is to support research to provide high throughput sequencing services for phytopathogenic fungi, plant insect pests and the associated host plants for use in genomic and transcriptome analysis. ARS desires the Cooperator to provide goods and services necessary to develop appropriate RNA, DNA and cDNA libraries from ARS provided material for sequencing. The cooperator will provide sequencing and data processing to ARS in the form of usable sequence data and all raw data.
1b.Approach (from AD-416):
The Cooperator under ARS direction will produce appropriate sequencing libraries from infected and noninfected control materials and conduct high throughput sequencing. ARS will provide Cooperator with isolated DNA and RNA. The cooperator will conduct initial alignment and comparison analysis and will send the data to ARS or to a third party designated by ARS.
This agreement was set up to provide collaborative sequencing services for SPCL, which supports the research of the parent project. Under this agreement, RNA was sequenced from resistant and susceptible cacao genotypes that were infected with the frosty pod pathogen. Non-infected controls were also sequenced. RNA from cacao plants, infected with frosty pod rot pathogens, with and without biocontrol organisms were sequenced. The corresponding controls for these combinations were also sequenced. These RNA sequences correlate to the genes that are being expressed in the organisms at a particular time. This information helps researchers understand how plants, pathogens and biocontrol organisms are interacting at the molecular level.