SOW.docx

Subject: Statement of Work for DNA isolation and Whole Genome Sequencing (WGS) of mango germplasm.

The USDA-SHRS, Miami, FL maintains a large collection of mango germplasm with several accessions displaying different horticultural characteristics. The overall objective of this project is to sequence mango germplasm using whole genome sequencing approach. This project requires isolation and quality check of DNA from 288 mango samples followed by sequencing and bioinformatics. The project will generate approximately 6000 Gbp DNA sequence data. This project will be completed by an outside vendor. Following are the tasks that will be performed in this project:

1) Mango leaf sample collection: Freshly growing new leaves and flowers will be collected from 288 mango trees in the field using a leaf sampling kit. This task will be performed by the staff at USDA-ARS, Subtropical Horticulture Research Station, Miami, Fl. Sampling kits with the tissues will be send out to an outside vendor who will perform the following tasks.

2) DNA isolation: DNA will be isolated by the vendor from all samples using standardized DNA isolation protocol from mangos leaves and flowers.

3) DNA quality check: DNA quality and quantity will be checked using standard procedures usually employing bioanalyzer and/or other procedures.

4) DNA library preparation: DNA samples will be sheared to approximately 300 bp and indexed with unique adapters, quality checked (QC), and sequencing libraries prepared and quality checked.

5) DNA library sequencing: All libraries will be sequenced using 2 X 150 PE reads on 2.1 NovaSeq 6000 S4 Cells to achieve 50X coverage of the approximately 439 Mbp mango genome. This will generate approximately 6000 Gbp in approximately 40 Billion 150X Paired End reads.

6) Bioinformatics: Reads will be demultiplex, quality checked (QC), and adapters trimmed. Bam mapping files will be generated and along with raw data from sequencing facility provided by the vendor.

7) DNA storage and return: DNA will be stored at -80 oC and provided by the vendor.