Sources_Sought_Notice_1.pdf

Sources Sought Notice PR0044050998 Seagrass Genome Sequencing Department of the Interior U.S. Geological Survey Pacific Islands Ecosystems Research Center

The U.S. Geological Survey is conducting market research to determine the availability of qualified businesses capable of providing seagrass genome sequencing services in accordance with the attached Statement of Work.

This Sources Sought Notice is for information and planning purposes only and does not constitute a solicitation. This is not a Request for Quote. The Government is not obligated to issue a solicitation or award a contract as a result of this notice. The Government will not reimburse any costs associated with responding.

The applicable North American Industry Classification System code is 541380 – Testing Laboratories and Services, with a size standard of $19.0 million. The applicable Product Service Code is B529 – Special Studies/Analysis: Scientific Data.

All responsible sources may submit a capability statement demonstrating their ability to meet the requirement. Responses shall be submitted via email to Joel Berberena at [joel_berberena@ios.doi.gov] and must be received before the close date of this notice.

Late responses or responses submitted by other than email will not be considered.

Capability Statement Requirements:

Interested vendors shall provide the following:

1. Description of laboratory capabilities for genome sequencing services.

2. Description of instrumentation, sequencing platforms, and analytical methods available to perform the attached Statement of Work.

3. Experience performing similar genome sequencing, plant genomics, transcriptomics, HiFi sequencing, Hi-C sequencing, Iso-Seq sequencing, or related scientific sequencing services.

4. Examples of similar work performed.

5. Description of quality control, quality assurance, and data delivery practices.

6. Company information, including business size, socioeconomic status, UEI, and SAM registration status.

7. Identification of whether the work would be performed in-house or through subcontractors.

The Government is seeking information on vendors capable of meeting the requirements in the attached Statement of Work. Responses will be used to determine the appropriate acquisition strategy, including whether this requirement can be set aside for small business participation.

Interested parties should only submit a response if they possess the technical capability, facilities, equipment, personnel, sequencing platforms, quality assurance processes, and experience necessary to perform the requirements identified in the attached Statement of Work. Responses that do not clearly demonstrate the respondent’s ability to perform the full requirement may be determined non-responsive for market research purposes and may not be considered in the Government’s acquisition planning. Vendors that cannot perform the required services, either directly or through a clearly identified teaming or subcontracting arrangement, should not submit a capability statement in response to this notice.

The requisition identifies the requirement as PR0044050998, Seagrass Genome Sequencing, for the USGS Pacific Islands Ecosystems Research Center. The attached Statement of Work contains the detailed technical requirements and deliverables.

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STATEMENT OF WORK

Seagrass Genome Sequencing Services

Brief Description The U.S. Geological Survey (USGS), Pacific Islands Ecosystems Research Center, requires genome sequencing services for seagrass tissue samples to support research on genomic diversity, clonality, and climate-resilient restoration of Enhalus acoroides and related seagrass species in Guam and surrounding Pacific islands. The contractor shall perform DNA and RNA extraction, sequencing library preparation, PacBio Revio HiFi and Iso-Seq sequencing, Arima Hi-C library preparation, Illumina sequencing, quality assurance checks, and electronic delivery of sequencing data and associated technical narratives.

1. Background The USGS Pacific Islands Ecosystems Research Center is conducting research to assess genomic diversity and clonality in seagrass beds in Guam and surrounding Pacific islands for climate-resilient restoration. The research requires genomic and transcriptomic sequencing of marine seagrass plant tissues, including Enhalus spp. and Halodule spp., to support reference genome assembly, annotation, and analysis of genes associated with resilience to heat stress, disease, turbidity, and other environmental stressors.

2. Objective The objective of this requirement is to obtain laboratory-based genome sequencing services, including DNA and RNA extraction, sequencing library preparation, sequencing, quality assurance, and electronic delivery of sequence data and technical documentation to the USGS.

3. Scope The contractor shall provide all labor, facilities, equipment, materials, sequencing platforms, reagents, quality assurance procedures, technical expertise, data processing, and electronic data transfer necessary to perform genome sequencing services for USGS-provided seagrass tissue samples.

The services shall include extraction of high-molecular-weight genomic DNA and high-quality RNA from flash-frozen seagrass leaves; preparation of HiFi, Arima Hi-C, and Iso-Seq libraries; sequencing using appropriate PacBio Revio and Illumina platforms; and delivery of sequence outputs and supporting narratives to the USGS.

4. Contractor Requirements

• Receive up to 5 grams of flash-frozen seagrass leaf tissue from the USGS.

• Perform genomic DNA extraction from submitted plant tissue, with up to two extraction attempts per sample as needed to obtain high-molecular-weight DNA.

• Perform RNA extraction from submitted plant tissue, with up to two extraction attempts per sample as needed to obtain high-quality RNA.

• Prepare high-fidelity long-read sequencing libraries from extracted genomic DNA.

• Sequence HiFi libraries using the PacBio Revio platform.

• Prepare Arima Hi-C libraries for chromosome-scale scaffolding support.

• Perform Illumina sequencing of Arima Hi-C libraries.

• Convert extracted RNA to cDNA using the Iso-Seq Express 2.0 kit or an equivalent process suitable for long-read transcriptome sequencing.

• Sequence Iso-Seq libraries using the PacBio Revio platform.

• Conduct quality assurance checks on DNA extractions, RNA extractions, sequencing libraries, Arima Hi-C products, and sequencing outputs, as needed.

• Notify the USGS if submitted sample material is insufficient, degraded, contaminated, or otherwise unsuitable to produce high-quality sequencing results.

• Provide all final sequence outputs and a technical narrative identifying any issues, limitations, quality concerns, or deviations from expected methods.

• Deliver all data electronically to the USGS.

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5. Deliverables Deliverable Quantity Description Genomic DNA extraction 2 High-molecular-weight genomic DNA extraction from seagrass tissue.

HiFi library preparation 2 PacBio-compatible high-fidelity long-read library preparation.

PacBio Revio SMRT Cell sequencing for HiFi data

2 Long-read HiFi sequencing data.

Arima Hi-C library preparation 2 Hi-C library preparation for genome scaffolding.

RNA extraction 2 High-quality RNA extraction from seagrass tissue.

cDNA synthesis / Iso-Seq preparation 2 cDNA synthesis using Iso-Seq Express 2.0 kit or equivalent.

PacBio Revio SMRT Cell sequencing for Iso-Seq

1 Full-length transcript sequencing data.

Illumina sequencing of Arima Hi-C libraries

2 Short-read Hi-C sequencing data.

Technical narrative 1 Narrative describing sequencing results, quality issues, and deviations, if any.

Electronic data delivery 1 Delivery of sequence files and associated documentation to USGS.

6. Place of Performance Laboratory work shall be performed at the contractor’s genomics facility. The USGS will ship samples to the contractor’s facility as coordinated between the USGS and the contractor.

7. Period of Performance The period of performance will be stated on the SF-18.

8. Government Furnished Property No Government-furnished equipment is anticipated. USGS-furnished seagrass tissue samples are the subject of the sequencing services and will be provided to the contractor for analysis. The contractor shall handle the samples only as necessary to perform the required laboratory services.

9. Government Furnished Information The USGS will provide sample identification information, relevant sample metadata, shipping information, and technical points of contact necessary for performance.

10. Inspection and Acceptance The Government will inspect deliverables for completeness, readability, and conformance with this Statement of Work. Acceptance will occur after the USGS confirms receipt of all required sequencing data, quality assurance information, and technical narratives.

Acceptance criteria include:

• All required sequence files are delivered electronically.

• Files are accessible and not corrupted.

• The technical narrative is provided.

• Any deviations, quality concerns, or failed extraction attempts are documented.

• Deliverables correspond to the required sample number and sequencing services.

11. Warranty and Correction of Defective Deliverables If delivered files are corrupted, incomplete, inaccessible, or not consistent with the required sequencing services, the contractor shall correct or re-deliver the affected files at no additional cost to the Government.

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12. Special Requirements The contractor shall notify the USGS before proceeding if the submitted material is insufficient, degraded, contaminated, or otherwise unsuitable for the required sequencing workflows. The contractor shall not substitute sequencing methods or materially alter the required workflow without Government approval.