JOFOC 143021240296_Redacted.pdf

Version 2.0 19Aug2020

SINGLE SOURCE or BRAND NAME DETERMINATION USING

SIMPLIFIED ACQUISITION PROCEDURES (SAP)

FOR AN ACTION NOT EXCEEDING THE SIMPLIFIED ACQUISITION THRESHOLD

(AUTHORITY: FAR 13.106-1(b)(1))

(PR/RFQ number: 143021-24-0233)

1. Agency and contracting activity. Department of Commerce, NOAA Acquisition and Grants Office (AGO), Fisheries OMB Field Delegates and Northeast Fisheries Science Center EAD / AqSEB

2. Description of supplies or services required to meet agency needs (including the estimated value).

Overview description of services:The National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Northeast Fisheries Science Center (NEFSC) is the research arm of NOAA Fisheries in the region. The Center plans, develops, and manages a multidisciplinary program of basic and applied research. Wild harvest of Atlantic sea scallops Placopecten magellanicus is the most lucrative commercial bivalve fishery in the US ($488 million USD annually), however sea scallop landings are projected to decline by 50% at the end of the century in part from ocean acidification (OA; elevated ρCO2). Adaptive genetic change can occur rapidly and offset consequences of environmental change yet depend on variation maintained within an existing population. Thus, population genetics are essential to improve accuracy of risk assessment models by examining the capacity for sensitive species to evolve and counteract long-term ecosystem-scale change. We collectively experience the prolific research initiatives enabled by publicized reference genomes for commercial bivalves (i.e.

Crassostrea and Mytilus sp.). To date, there is no reference genome for sea scallops P. magellanicus, however the few existing studies postulate that there is high genetic differentiation between sea scallops in the Mid-Atlantic bight (MAB) and the Gulf of Maine (GOM). Expansion of this thread is key, as warming will press populations poleward and shift wild harvesters to cooler, more-acidified systems such as the GOM. An assembled and annotated genome will be an invaluable product for end-users and will catalyze research initiatives, such work is dependent on the rigor of assembly and annotation. A continuous genome and gene annotation will be generated using whole-genome sequencing of short-read DNA (Illumina Hi-C Library) and long-read DNA platforms (PacBio Sequencing Revio) and RNA sequencing (Illumina NovaSeqX plus, PE150), each with a tissue sample from the same individual scallop. Because of the need for a reliable assembly, subsequent services are planned for quality assurance via re-sequencing (i.e. low-coverage whole genome sequencing), DNA assembly (i.e. PacBio Assembly with misjoin detection/correction), haplotyping analysis (phasing services), and gene calling. Ultimately, an assembled and annotated Atlantic sea scallop genome will enable cost effective –omics approaches to sustain a viable blue economy in the North Atlantic. End-users of the reference genome include evolutionary biologists and fisheries management/modelers and will permit exploration into possible solutions, such as assisted gene flow, sanctuaries, and rotated fishing grounds.

Scope of work: Contractor shall provide all trained labor, equipment, materials, supervision, transportation, permits, insurance, and quality control necessary to provide extraction, library preparation, and Next-Generation Sequencing of preserved tissues for Illumina and PacBio platforms. Contractor shall provide haplotype analysis, resequencing, assembly, and annotation/gene calling services. Performance under this contract known as “Work”. Contractor shall be fully knowledgeable of all contract requirements and shall ensure Work is accomplished in accordance with the terms and conditions of the contract in a manner that will promote and maintain a safe environment.

Services required: We require one contact task in the base year, encompassing different sequencing platforms and bioinformatic services to accommodate chromosome-scale assembly and annotation from the vendor. Pacbio and Hi-C technologies are required for these sequencing approaches to keep with industry standards for shellfish genome assembly and annotation. They are as follows:

(Insert PR/RFQ number, as applicable)

Task 1: DNA and RNA extractions, library preparation, and sequencing and subsequent genome assembly and annotation. Review the following services and specific requirements:

a. Must be able to receive tissue samples on dry ice, with or without fixative added (ethanol or RNAlater)

b. Must use the same individual scallop for task 1 (both library preparations within task 1)

c. HMW-DNA extraction and QC. Extraction using PacBio NanoBind PanDNA kit (PacBio, 103-260-000), DNA QC using Qubit, and fragmentation (if applicable) using Megaruptor 3.

Evaluation of fragment sizes with Agilent TapeStation.

d. PacBio library preparation and sequencing. Use PacBio SMRTbell® prep kit 3.0 with the SMRTbell® barcoded adapter plate 3.02 for library preparation and sequence the library on PacBio Revio

e. Hi-C library preparation and sequencing. Use Proximo Hi-C 4.0 Kit and sequence the Hi-C library ~100M read-pairs on Illumina NovaSeqX plus PE150

f. Low coverage DNA sequencing for library quality assurance (<1M paired end Illumina reads).

Prior to production sequencing, determine library performance by low-pass sequencing. Generate ~200,000 read pairs of sequencing data on an Illumina iSeq and map to the reference assembly

g. PacBio genome assembly with misjoin detection and correction, using PacBio Hifi long reads

h. Phasing services. Use the Hi-C data to phase the assemblies producing a draft for each haplotype

i. RNA extraction and purification. QC quantification using Qubit RNA HS and fragment analysis with Agilent Bioanalyzer RNA 600 pico

j. RNAseq library preparation. cDNA synthesis with NEBNext® Ultra II Directional Library Prep Kit for Illumina. QC quantification using Qubit RNA HS and fragment analysis with Agilent Bioanalyzer RNA 600 pico

k. RNA-seq on Illumina NovaSeqX plus, PE150

l. Phase Genomics Proximo™Genome Scaffolding Platform for assembly for medium genome

m. Gene calling and annotation. This service includes alignment of RNA-seq reads to the genome assembly validated by >1 method (such as STAR and RepeatModeler, using the NCBI), masking repeats in the assembly using RepeatMasker. Apply MAKER to use repeat families generated from RepeatModeler, RNA-seq alignments from STAR, and the UniProt functional protein sequence database as evidence for gene annotation. Include a second round of annotation for ab initio gene prediction using AUGUSTUS. Finalize functional annotation with MAKER using the UniProt functional protein sequence database. Assess final scaffolds using BUSCO.

Expected delivery/date period of performance: A FASTA containing the chromosome-scale genome assembly and csv file containing genome sequencing stats. An annotation file containing gene calls and annotation. Required no later than four months from the time of sample submission.

Contract type: Service

3. Identification of the single source or the brand name to be solicited.

Phase Genomics 1617 8th Avenue N Seattle, WA, 98109

4. Supporting rationale. Only one source or brand name is reasonably available as detailed below:

■ Brand Name – This particular brand name is essential to the requirement and market research indicates similar products do not meet or cannot be modified to meet agency needs. Phase genomics is essential to our required sequencing platforms, phase services, annotation, and deliverables. Phase has a resounding reputation for novel use of Proximo™Genome Scaffolding Platform that uses proximity ligation to capture chromosomal origin of sequences and ensure contiguous and high-quality assemblies. Phase Genomics has used their Proximo™ Platform to publish the human genome as well as animal models integral to agriculture (goat and honey bee), and genomics research (giant clam, stickleback, firefly, clownfish), to name a few. .

□ Compatibility to existing systems or equipment - The required supplies must be compatible in all aspects (form, fit, and function) with existing systems or equipment, and the source is uniquely qualified to meet the requirement.

■ Exclusive Licensing Agreement/Restrictive Rights/Authorized Reseller - The source has one or more of the following: an established exclusive licensing agreement, proprietary data, limited rights in data, patent rights, OEM required certifications or OEM authorized reseller, copyrights or secret processes with regard to the supplies or services required. Phase Genomics has rights to their Proximo™Genome Scaffolding Platform. Sole source contracting Phase will ensure cutting edge technologies and services are employed to expedite a publishable genome resource and ensure high quality deliverable required for this project.

□ Urgency – The nature of the requirement has been deemed urgent due to unusual and compelling circumstances. Following competitive procedures would result in unacceptable delays resulting in serious injury to the Government.

■ Other - Only one source is capable - Phase has rights to their Proximo™Genome Scaffolding Platform, in addition to their sequence on multiple platforms (Illumina NovaSeq and PacBio Revio), resequencing for quality assurance, and bioinformatic annotation and assembly. Sole source contracting Phase will ensure cutt edge technologies and services are employed to expedite a publishable genome resource.

5. Market Research.

To our knowledge, no other companies have proven track records and ability to complete the work required for this project.

6. Technical/Requirements Representative Certification

I certify that this requirement constitutes the Government’s minimum needs and the supporting data provided herein is accurate and complete to the best of my knowledge and belief.

Director NEFSC

Note that NOAA Fisheries policy requires these sole source documents to be signed by a regional administrator, science center director, or Deputy director. See MB Guidance: Sole Source Actions.

7. Determination (Required) I hereby determine that the circumstances of this action deem only one source is reasonably available. This determination is accurate and complete to the best of my knowledge and belief.

(Insert name) Date Contracting Officer