Genome Sequencing

Background
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 depends 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. 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.

Work Details
The contractor shall provide Next-Generation Sequencing of long- and short-read DNA and RNA for draft genome assembly and annotation. The services include DNA and RNA extractions, library preparation, sequencing, genome assembly, haplotype analysis, resequencing, gene calling, and annotation. The contractor must be fully trained authorized service provider of Next Generation Sequencing on PacBio Revio and Illumina platforms HiSeq and NovaSeq S4. The contractor shall perform specific tasks including RNA extraction services, RNA Library preparation, sequencing services for RNA sequences, HMW-DNA extraction services, PacBio Library Preparation, Hi-C Library Preparation, low coverage sequencing for library QC (<1M paired end Illumina reads), Illumina Sequencing of Hi-C Library (~100M Read-Pairs), PacBio sequencing Revio, PacBio Assembly with misjoin detection and correction (Genome Haplotyping Analysis), Phasing Service, Proximo assembly for a medium genome, Gene calling and annotation.

Period of Performance
(1) Base year with no option years. Contractor shall deliver sequences to NEFSC within 4 months of sample submission and no later than August 31, 2025 for all CLINS.

Place of Performance
At Vendor's Location.