Location: Sustainable Agricultural Systems Laboratory
Project Number: 8042-21220-259-003-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2020
End Date: Aug 31, 2025
Objective:
The objective of this agreement is to support research through collaborations that provide high throughput next generation sequencing and genotyping by sequencing services for phytopathogenic and Phyto beneficial fungi and bacteria and their associated host plants. The data generated through the collaboration will be used in genomic and transcriptome analysis and genetic diversity analysis. ARS desires the Cooperator to provide goods and services necessary to develop appropriate RNA, DNA, and cDNA libraries from ARS provided materials. The Cooperator will provide sequencing and data processing to ARS in the form of usable sequencing data, bioinformatic analysis, as well as providing the raw data.
The objectives of the agreement directly relate to specific project objectives: “Use functional omics (genomics, transcriptomics, proteomics, and metabolomics) approaches to identify biological control mechanisms involved in control of sclerotial plant pathogens” in the project “Biologically Based Technologies for Control of Soil-Borne Pathogens of Vegetables and Ornamentals”.
Approach:
ARS will provide the Cooperator with the source materials or isolated DNA and or RNA. The Cooperator under ARS direction will produce appropriate(PacBio/ Nanopore/Illumina) libraries for sequencing or from pathogen associated or not associated control material and conduct high throughput sequencing. The Cooperators will conduct alignment, assembly, genome annotation, variant calling and Phylogeny analysis, and comparison analysis and will send the data to ARS or to a third party designated by ARS.
