Sources Sought for Sequencing of Wild Pea, Pisum fulvum - PfNa27 Reference Genome

This is a Sources Sought notice Only.  This is NOT a solicitation for proposals, proposal abstracts, or quotations.  This Sources Sought is issued for information and planning purposes only as part of USDA ARS market research and does not itself constitute an RFQ. This requirement is covered under NAICS code 541714. The purpose of this notice is to obtain information regarding the availability and capability of qualified sources; Small Businesses; HUBZone small business; service-disabled, veteran-owned small business; 8(a) small business; veteran-owned small business; woman-owned small business; or small disadvantaged businesses; Responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible.

The Sequence and assembly of high-quality complete reference genome with annotated transcriptome of USDA ARS Accession Number PI 343996 pea Pisum sativum subspecies elatius using the PacBio Revio system high-density 25 million ZMW SMRT cells delivering HiFi reads.  Work to include library construction frozen plant tissue using the Dovetail Hi-C Kit. Expected product will include the yield for CCS sequencing of 60-90Gb for the pea DNA per lane and a final yield of 2.5 billion read pairs and 750Gb of raw data per lane. Gene and protein annotation will be included.  In addition, RNA prep from frozen plant tissue (8 different plant tissues, see list below), RNASeq library construction and sequencing of up to 40 million read pairs per sample using Stranded HT, Illumina Sequencing on a NovaSeq 6000 PE150. Data for the complete genome annotation will be delivered as GFF, cDNA and protein files for each pea sample (haplotype). Base pair call accuracy of 99.9% (Q30 or greater). 

For each genotype, the sequencing costs $189.00 for first 10 Gb and $95.00 for each incremental 10Gb.  Therefore, for 40Gb data, the total cost per genotype is $474 [189 + (3*95)].  Total cost for sequencing, genome assembly and annotation is $42,330.

Tissues that will be sequenced (RNA):

• Leaf (expanding tissue)
• Stem
• Petiole
• Root
• Nodule
• Flower Bud
• Young pod (pre-filling)
• Seed (filling stage)

The whole genome sequencing and genome assembly with RNA transcriptome and short-read error-detection is required for PI pea Pisum sativum genotypes (USDA accessions) in order to identify the specific genes conferring high levels of genetic resistances to diseases in Pisum sativum subspecies elatius and contribute to assembly of a Pan-Genome of Pisum sativum species complex.  Pea has a relatively large genome (4.5 Gb) with +80% long repeats of repetitive DNA stretches so both high density and very long-read sequencing technology is necessary.

Capability Statement

All information submitted in response to this announcement is voluntary, and the Government will not pay for information requested nor will it compensate any respondent for any cost incurred in developing information provided to the Government. Business concerns that possess the capabilities necessary to undertake this work should submit complete documentation of their capabilities to the Contracting Officer.  Capability statements shall include the Contractors contact point to discuss their response.

The capability statement should include:

1)  Acknowledgement that they are able to provide the subject supplies/services being requested;

2) Interested vendors should identify their size standards in accordance with the Small Business Administration;

3) At least three previous requirements that are similar to the requirement include a discussion of the Contract type, delivery method, duration, etc.;

4) Any other information considered relevant to this requirement; and

5) The government requests that no proprietary, classified, confidential, or sensitive information should be included in the response.

Any vendor responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine their qualifications to perform the work.  Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted.  After review of the responses received, a combined synopsis/solicitation may be published on sam.gov depending on the responses received.

All responses to this Sources Sought Notice must be received by the notice’s POC by the deadline in order to be considered. Responses may not be returned. Responders are solely responsible for all expenses associated with responding to this Inquiry. Do not submit pricing information in response to this Request.