Tropical Plant Genome Sequencing

Goals / Objectives
The objective of this agreement is to support research through collaborations that provide high throughput next generation sequencing link to novel genome assemblage that can accurately reconstruct the entire genome down to the chromosomal and DNA strain level for tropical and semitropical plants; phytopathogenic fungi and bacteria; plant insect pests and their associated host plants. The data generated through the collaboration will be used in genetic diversity analysis. ARS desires the Cooperator to provide goods and services necessary to develop appropriate DNA libraries from ARS provided materials for next generation sequencing. The Cooperator will provide sequence data analysis to ARS in the form of usable sequence, genome assemblages and SNP data as well as providing the raw data. The objectives of the agreement directly relate to specific project Objective 1. â¿¿In collaboration with domestic and international cooperators, characterize genotypically and evaluate phenotypically priority cacao and coffee genetic resources, breeding stocks, and cultivars, and disseminate data via the projectâ¿¿s website, genetic resource or genomic databases, and GRIN-Globalâ¿ and Objective 2: â¿¿Conduct research to develop genomic tools and approaches and then apply them to improving the efficacy of genetic resource management of other tropical perennial crops, such as sugarcane, tea, Annona, Garcinia, peach palm, pitaya, sapodilla, and sapoteâ¿.

Project Methods
The Cooperator under ARS direction will produce appropriate sequencing libraries for sequencing and conduct high throughput sequencing and assemble the genome using proprietary methods and bioinformatics tools. When needed, the Cooperator may be asked to reassemble a previously sequenced genome and, in that case, ARS will provide the Cooperator with raw sequence reads. For full genome assemblage, ARS will provide the Cooperator with isolated freeze-dried plant and/or fungal material. The Cooperators will conduct DNA extraction, library construction, alignments and genome assemblage analysis and will send the data to ARS or to a third party designated by ARS.