A04_SOW_Dovetail_Genomics_OmniC_RNA_Seq 1232SA26Q0708.docx
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- Solicitation number
- 1232SA26Q0708
About this file
This is a Statement of Work (SOW) for a USDA Agricultural Research Service contract to generate genomic resources for Pecan and Hickory (Carya species) cultivar development. The contractor must perform Omni-C and RNA sequencing on 15 Pecan or Hickory accessions to produce high-quality, chromosome-scale genome assemblies and RNA sequences for genome annotation. The technical scope requires the contractor to extract nuclei from young leaf tissue samples provided by the government, construct Omni-C libraries targeting 30x coverage per haplotype with PE150 reads using appropriate sequencing technology (targeting ~670-800 Mb genome size with 16 chromosomes), sequence approximately 2M PE 75bp reads for library quality assessment, extract RNA with rRNA depletion, and sequence RNA libraries to approximately 20M read pairs per sample on an Illumina platform. The contractor shall scaffold the government-provided draft assemblies to chromosome-scale using the Dovetail HiRise software pipeline and may perform TAD (Topologically Associating Domains) analysis if specified conditions are met.
All deliverables must be completed within nine months and include 15 HiRise assemblies in FASTA format with detailed reports on assembly statistics, Omni-C library features, linkage density plots, scaffold break details, BAM files with mapped read alignments, TAD analysis outputs (at 10kbp, 25kbp, and 50kbp resolutions, CTCF binding sites, compartmental organization, and isochore locations), and 24 pairs of FASTQ files containing approximately 20M read pairs each from RNA sequencing with a QC report. The related RFQ (solicitation number 1232SA26Q0708) is unrestricted to all responsible sources, requires vendor registration in SAM.gov at submission and award, and specifies quotes are due by 4:00 a.m. Central Standard Time on Friday, July 3, 2026, with questions due by 3:00 a.m. on Tuesday, June 30, 2026. Quotes must be submitted electronically to lynn.hults@usda.gov and include detailed descriptions of relevant experience and past performance; quotes lacking substantive information beyond specifications will not be considered. The government retains all rights to data produced and prohibits unauthorized disclosure or use.
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US Department of Agriculture (USDA)
Statement of Work
Contents
| Project | 3 |
| General Information | 3 |
| 1.0 Scope of Work | 3 |
| 2.0 Background | 3 |
| Contractor Requirements | 3 |
| 3.0 Technical Requirements / Tasks | 3 |
| 4.0 Government Furnished | 3 |
| 5.0 Deliverables / Schedule | 3 |
| 6.0 Travel | 4 |
| 7.0 Contractor’s Key Personnel | 4 |
| 8.0 Security Requirements | 4 |
| 9.0 Data Rights | 4 |
| 10.0 Section 508 – Electronic and Information Technology Standards | 4 |
| Attachment | 4 |
Project Dovetail Genomics Omni-C and RNA-seq package for Pecans & Hickories
General Information
1.0 Scope of Work
The objective of this project is to perform Omni-C and RNA sequencing of 15 Pecan or Hickory (Carya sp.) accessions and to provide HiRise genome assemblies (N=15) and RNA sequences for genome annotation.
2.0 Background
We are beginning a project to generate genomic resources for Pecan cultivar development using sequences from Pecans and Hickories. The study investigates 15 species of Carya (Hickories sensu lato). We have sequenced genomes using HiFi and ONT-long read data, but require improved assemblies with Omni-C reads to generate high-quality chromosome scale assemblies. We also require RNA sequences for genome annotation. We aim to use these improved assemblies to gain insight to the genetic basis of phenotypes across Carya.
Contractor Requirements
3.0 Technical Requirements / Tasks
DNA/Tissue: The contract may perform a nuclei extraction or fix tissue for CCC library from young leaf samples of Carya or other species submitted by the Government.
Library Preparation and Sequencing: The contractor shall construct Omni-C libraries to target 30x coverage per haplotype of PE150 reads using an appropriate technology (e.g. Illumina). This is based on the genome size provided by the Government (~670 Mb to 800 Mb and 16 chromosomes for Carya sp.). The contractor shall sequence ~2M PE 75bp reads and map the data back to the draft assembly to assess library quality.
RNA Sequencing Library Preparation: The contractor shall extract RNA and prepare a standard RNA library with rRNA depletion. Contractor shall communicate with the government for samples that have a RIN below 7. PE 150bp reads shall be sequenced on an Illumina platform to the target of ~20M read pairs per sample. Tissue will be provided by the government. Sequence reads will be returned to the government in a suitable format with sequencing results.
Informatics Package: The contractor shall take provided assemblies and scaffold them to generate chromosome scale assemblies (N=15). The contractor shall QC assemblies and provide results and reports files, and the final assembly. The contractor shall scaffold the through a Dovetail HiRise software pipeline using Omni-C library data.
The contractor shall consult with the government for the performance of TAD analysis on the genome generated from Omni-C libraries if 40% of read pairs should map at a distance of greater than 1 Kbp, genome size is less than 10 Gb, assembly scaffold size is less than 400 Mbp, more than 40% of the genome is uniquely mappable, and coverage is 100 M read pairs per 1 Gb.
4.0 Government Furnished
The government will furnish leaf tissue of the plant species in quantities sufficient for the contractor to perform the work. The Government shall further furnish tissue from leaves, roots, flowers, embryos, fruits, and seeds, or other tissues, in sufficient quantities for RNA sequencing.
5.0 Deliverables / Schedule
The contractor shall furnish within 9 months the following:
• HiRise Assembly deliverables:
• The HiRise assembly in FASTA format
• A report summarizing key assembly statistics, features of the Omni-C library, and a linkage density plot of the proximity ligation library data
• A table detailing the breaks made to the input scaffolds
• A table describing the position of the input assembly scaffolds within the final HiRise scaffolds
• BAM file(s) containing alignments of the Omni-C library read pairs mapped to the draft assembly
• TAD Analysis deliverables (pending consultation):
• TAD calls at 10kbp, 25kbp, and 50kbp
• CTCF binding sites
• A/B compartmental organization
· Isochore locations
· Guide to loading and viewing data in HiGlass
• Summary report
• RNA Sequencing Library deliverables includes twenty-four (24) pairs of FASTQ files, each containing ~20M read pairs.
• QC report
• Raw ILMN data from deep sequencing the Omni-C library
6.0 Travel
N/A
7.0 Contractor’s Key Personnel
N/A
8.0 Security Requirements
N/A
9.0 Data Rights
The government will retain all rights to data produced, furnished, acquired, or used in meeting contract requirements. Disclosure, use, or production of data without permission from the government is prohibited.
10.0 Section 508 – Electronic and Information Technology Standards N/A
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