Statement of Work.pdf

STATEMENT OF WORK

Long Read Whole genome sequencing of Phyllachora maydis, a causal agent of Tar Spot of Corn

General Information

1.0 Scope of Work:

The service provider will prepare and quality control Phyllachora maydis whole genome library (350bp) and Pacbio sequel II DNA CLR library, perform NovaSeq PE150 and Pacbio sequel II (CLR mode) sequencings, and provide NovaSeq PE150 (3 G raw data per sample) and Pacbio sequel II (CLR mode) (5 G raw data per sample) sequencing data, data quality control, and provide PacBio data summary report, PacBio de novo genome assembly report and assembled contigs, BAM raw data files. DNA samples for Pacbio and Novaseq PE150 will be provided by the Crop Production and Pest Control Research Unit (CPPC) at Purdue University in West Lafayette, Indiana. One of the major goals of this ARS project is to generate high-quality near-complete Phyllachora maydis genome assemblies.

The improved genome sequence will improve gene annotation and allow genes for pathogenicity to be identified and their potential host targets analyzed.

2.0 Background:

The laboratory has analyzed and published a draft genome sequence of Phyllachora maydis in collaboration with Purdue Extension Pathologist Darcy Telenko (Telenko et al., 2020) but it was made with Illumina technology so the genome is likely to contain many gaps and not all gene models may be complete. The primary objective of the present work is to generate a contagious and complete assembly with improved genome coverage. The improved genome sequence of Phyllachora maydis will improve gene annotation.

CONTRACTOR REQUIREMENTS

3.0 Technical Objectives and Tasks:

Features, Components, Accessories, Modules, Software and/or Services to be included:

• Analyze High molecular weight DNA sample quality and quantity as required for third generation sequencing.

• Construct Phyllachora maydis whole genome library preparation (350bp)

• Construct Phyllachora maydis Pacbio sequel II DNA CLR library

• Perform quality of Phyllachora maydis whole genome library and Pacbio sequel II DNA CLR library

• Provide NovaSeq PE150 (3 G raw data per sample) and Pacbio sequel II (CLR mode) (5 G raw data per sample) sequencing

• Perform data quality control

• Provide PacBio data summary report, PacBio de novo genome assembly report and assembled contigs, BAM raw data files

• Delivery schedule: 40 days from the time of sample submission

4.0 Government Furnished: Extracted high molecular weight DNA (more than 20 kb) sample will be shipped to the vendor.

5.0 Deliverables / Schedule: NovaSeq PE150 (3 G raw data per sample) and Pacbio sequel II (CLR mode) (5 G raw data per sample) files will be provided which include Provide PacBio and NovaSeq PE150 data summary reports, PacBio and NovaSeq PE150 de novo genome assembly reports and assembled contigs, BAM raw data files.

6.0 Travel: Not Applicable

7.0 Contractor’s Key Personnel: Contractor’s personnel will be highly trained and experienced in order to perform the high molecular weight DNA quality controls, NovaSeq PE 150 and Pacbio sequel II (CLR mode) sequencings, sequencings data quality control, NovaSeq and PacBio denovo genome assembly and contings assembly.

8.0 Security Requirements: Not Applicable

9.0 Data Rights: USDA retain the rights to NovaSeq and PacBio denovo genome assembly and contings assembly data files provided by the contractor.