SOW_genome_annotation_1.doc

PERFORMANCE-BASED WORK STATEMENT

I. GENERAL INFORMATION

A. Introduction.

The overall goal of the work is to produce an assembled and annotated reference genome for the rough-skinned newt, Taricha granulosa, submitted to NCBI. Given the estimated size of the genome (36 GB), and the relatively high proportion of repetitive content (~70%), we estimated that the assembly and annotation will take an expert up to six months to complete.

B. Background.

Amphibians are among the last of the vertebrates to enter the whole-genome sequencing phase due to the large size and high percentage of repetitive sequence content in their genomes (Liedtke et al., 2018; Womack et al., 2022). However, decreasing sequencing costs and advances in assembly methods have permitted researchers to invest in new reference genomes for a small but growing set of amphibian species. For example, the genomes of Rana draytonii and Hyliola regilla are currently being assembled as part of the California Conservation Genomics Project. Nevertheless, challenges to building amphibian genome resources remain. Despite California being a hotspot for salamander diversity, salamanders were completely excluded from CCGP efforts because their genomes are very large (>30 GB) and thus expensive to build. The work needed would help produce the data that are necessary to build a reference genome for the rough-skinned newt, Taricha granulosa. Reference genomes are necessary for modern conservation programs and critical for any state-of-the-art research program and there is concern that some populations are now showing invasiveness through hybridization (Matthews and Vosshall, 2020).

C. Definitions/Applicable Documents.

Reference genome: an assembly of all DNA from a single individual of a species into a set of sequences that span each chromosome. The format is usually fasta or GenBank.

Annotation: a compilation of gene locations within the genome overlaid on the sequence. The format is usually gff3 or gff

D. Scope.

The scope of the work is assembly and annotation of PacBio, Oxford Nanopore, and Illumina sequence data from Taricha granulosa into a reference genome.

II. WORK REQUIREMENTS

A.

Technical Requirements.

1. Describe specific work requirements and/or work products.

Phase 1: Preliminary assembly using established bioinformatic pipelines (e.g., Hifiasm).

Phase 2: Curated assembly with manual editing (e.g., in Juicer)

Phase 3: Annotation (e.g., using NCBI annotation pipeline)

Phase 4: Review and revision of product, if needed

2. Criteria for acceptance of Product or Service.

The product should meet or nearly meet the Vertebrate Genome Project and G10K standards: contig N50 of 1 million bp (1Mb), scaffold N50 of 10Mb, 90% of the genome assembled into chromosomes confirmed by 2 independent sources, a base-call quality error of no less than QV40 (no more than 1 nucleotide error in 10,000 bp), and haplotype phased.

B.

Deliverables.

1. Characteristics for work product described in II.A.1., identified by name and quantity.

The genome and its annotation should be uploaded to NCBI. Details regarding specifics are described in II.A.2

2. Delivery dates for work/product to be completed and point of delivery.

February 2026

III.

SUPPORTING INFORMATION

A. Place of Performance: Vendor’s facility B. Period of Performance: June 2025 – February 2026

C. Government Furnished Property (GFP): N/A

D.

Special Considerations.

1. Key personnel qualifications (researchers, instructors, writers, project managers, programmers, etc.)

Experience assembling a variety of difficult genomes de novo

2. Data Rights, Safety, Environment.

Data will be uploaded to the NCBI database and made publicly available by February 2027.

3. Security/Privacy issues (ingress to Federal buildings, personnel clearances, computer security).

N/A