Notice of Intent to negotiate sole source contract with Texas A&M University Corpus Christi

Description

Special Notice: FD-2026-358 NOAA/NMFS/SEFSC The U.S. Department of Commerce (DOC), National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Southeast Fisheries Science Center, intends to award, on a sole source basis, under the authority of FAR 13.106-1(b)(1), with Texas A&M University Corpus Christi of Corpus Christi, Texas to procure the following: The focus of this requirement is the efficient discovery of markers for accurate kinship assignment requires a high-quality genome, which does not currently exist for the sandbar shark. To develop a high-quality reference genome, high-coverage DNA sequencing of a single male of each species will be performed. High molecular weight DNA will be extracted from heart tissue, and a combination of DNA sequencing technologies will be used to sequence the genome with high accuracy and contiguity. First, Pacific Biosciences (PacBio) long-read sequencing will be used to generate long, accurate sequence scaffolds assembled using the canu software (Koren et al., 2017). Subsequently, chromosome conformation capture (Hi-C) sequencing will be used to assemble PacBio scaffolds into a near chromosome-scale assembly (Korbel & Lee, 2013). Finally optical density mapping will be used to ensure proper assembly of chromosomes (Yaun et al. 2020), an important step for organisms with large genomes and repetitive content. Differences in genomic architecture among individuals (e.g., large indels, inversions) are important features of genomes that cannot be characterized using a single genome sequence. Therefore, we will also resequence the genomes of 20 individuals at moderate-depth (~20x) following protocols outlined in Jones et al. (2023). Briefly, high molecular weight DNA will be extracted using the Mag Bind Blood and Tissue Kit (Omega Bio-Tek), quantified and standardized to 2 ng/�l. For each individual sample, ~5 ng of DNA will be fragmented and tagged with adapter sequences, using the Illumina DNA Prep Kit. Polymerase chain-reaction (PCR) amplification of fragments will then be performed to incorporate sequences necessary for Illumina flow cell annealing, while adding index sequences. The incorporation of index sequences enables DNA from multiple individuals to be sequenced simultaneously and each individual to be identified unequivocally. Products are then cleaned and pooled into a single library, containing 20 individuals. which will be sequenced at 20x coverage across three lanes of a NovaSeq platform. The applicable Size Standard is North American Industry Classification System (NAICS) Code 541380, with a Small Business size standard of $19M. The Government intends to negotiate a firm fixed price contract. This Special Notice of intent is not a request for competitive proposals and no solicitation package is available. However, firms that believe they can fully meet the Government's requirements may submit substantiating documentation in writing. Submissions are due within 15 days of this posting. Oral communications are not acceptable in response to this notice. Responses may be emailed to amy.gilliland@noaa.gov. Such documentation will be evaluated solely for the purpose of determining whether or not to conduct this procurement on a competitive basis. A determination by the Government not to compete this requirement based upon responses to this notice is solely within the discretion of the Government. It is the Government's belief that only can Texas A&M University Corpus Christi can provide the requirement stated above. Attachment: Single Source Determination The contractor will analyze previously collected tissue samples for sandbar shark to develop high-quality genome, which does not currently exist for the sandbar shark. This is necessary to further research on determining a population size for sandbar shark using close-kin mark recapture and age structure of the population using epigenetics. These projects are a priority for NOAA Fisheries to further the use of Omics in population assessment. To develop a high-quality reference genome, high-coverage DNA sequencing of a single male will be performed. High molecular weight DNA will be extracted from heart tissue, and a combination of DNA sequencing technologies will be used to sequence the genome with high accuracy and contiguity.