WGSsequencing_Quinn_2024_SOW.docx

US Department of Agriculture (USDA)

Statement of Work

Project Library construction and whole genome sequencing for species of conservation concern

General Information

1.0 Scope of Work

The purpose of this service is to prepare genomic libraries from DNA extracts and generate high-coverage whole-genome sequence data for terrestrial species of conservation concern.

2.0 Background

To evaluate the genetic health of isolated and fragmented wildlife populations in the United States, whole genomes will be sequenced from 100 tissue samples that are archived at the National Genomics Center for Fish and Wildlife Conservation (NGC). The primary focus is wolverine (Gulo gulo), a federally listed Distinct Population Segment in the U.S., but additional preliminary sequences will be generated for other species of conservation concern, such as lynx (Lynx canadensis) and marten (Martes americana and Martes caurina).

To generate high-quality sequence data, we require the technical capabilities of a in a CLIA-certified and CAP-accredited laboratory. The contracted laboratory will a) evaluate the quality of the genomic DNA that the NGC provides, b) construct libraries from the provided genomic DNA, and c) generate high quality sequence data from the prepared libraries on a high-throughput Illumina platform.

The DNA samples for wolverines and other species are limited in quantity and vary in quality and degree of degradation. We therefore require a laboratory with the flexibility and expertise to construct libraries from degraded and/or low-quantity DNA (e.g., <100 ng). Additionally, sequencing genomic data on different lanes or platforms has the potential to introduce “batch effects” that can mask biological signals—we therefore are seeking compatibility with previous whole genome datasets and complete control as to how and which sample libraries are pooled together within a sequencing lane.

Contractor Requirements

3.0 Technical Requirements / Tasks

The technical methodologies to be used to generate genomic data from these taxa are as follows; all work will be performed by a commercial laboratory without government supervision.

· DNA extracts from specimens provided by Catherine Quinn at the NGC will be evaluated for quantity (e.g., using a qubit fluorometer), contamination from proteins or RNA, and distribution of fragment sizes (e.g., electrophoresis gel or tapestation)

· Sequencing libraries will then be prepared from DNA extracts using a standard PCR-based, Illumina-compatible protocol with dual indices.

· Libraries will be evaluated for quality (e.g., library concentrations, distribution of insert sizes) and researchers will determine which to proceed with sequencing.

· Selected libraries will be pooled for sequencing on lanes according to the researcher’s specifications.

· Pooled libraries will be run on a Novaseq X Plus 25B in concentrations that result in an average of 40 Gigabases or more of sequence data per sample.

· Sequence data will be de-multiplexed based on dual indices unique to each sample.

· Raw, de-multiplexed sequence data will be provided to Catherin Quinn

· Project updates will be given at completed project milestones (DNA quality assessment, library preparation, sequencing)

4.0 Government Furnished

There is no government furnished support other than funding to the company to perform DNA sample processing.

5.0 Deliverables / Schedule

The deliverables/schedule are as follows:

1) Notification of DNA sample quality 1-2 weeks after samples are received.

2) Notification of library quality assessment after libraries construction has been completed (expected within 4 weeks after samples are received)

3) Data files containing all sequenced reads in fastq format will be provided 4-14 weeks after samples are received.

Example 1 Key Deliverables

6.0 Travel

There is no travel associated with this PO.

7.0 Contractor’s Key Personnel

Will be identified once contract is awarded.

8.0 Security Requirements

There are no Security Requirements

9.0 Data Rights

Data generated is the property of USDA-USFS

10.0 Section 508 – Electronic and Information Technology Standards There is no Information Technology to be Acquired.

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