CEFAS24-126 RFQ for Genotype-by-sequencing approach of Colossal Squid

Description

Cefas is currently undertaking a population genetics assessment on colossal squid. Cefas is seeking a supplier to sequence rare samples using a genotype-by-sequencing (GBS) approach. Tissue samples (mainly tentacles) have been collected from various regions across the globe. The samples themselves are in two types of preservative, depending on the institutes which collected the samples; ethanol and formaldehyde.

Cefas is aware that there is a multitude of genotype-by-sequencing approaches, some using propriety technology and some not. We are seeking applications which offer a GBS approach that maximises SNP identification and coverage to allow Cefas explore population structure. Additionally, suppliers must have a comprehensive DNA extraction step to compensate for varying levels of sample preservation.

Due to the scarcity of these animals, we have 33 samples but we expect samples to be run in duplicate at an average coverage of x30 depth for each duplicated sample.

Requirement:
To aid with the above project, Cefas require DNA extraction of squid tissues in ethanol (31) and formaldehyde (2). Assessment of DNA quantity and quality (see 'Deliverables' sections) will need to be completed and discussed with Cefas before genotype-by-sequencing of squid samples begins. Cefas are seeking the highest sequencing coverage possible to compensate for minimum samples sizes. Therefore, suppliers are asked to provide a cost per individual sample (n=66, in total).

The colossal squid currently has no reference genome. For the benefit of potential suppliers considering which restriction enzymes to use, we supply the following genome information of two closely related species;

Estimate genome size = 3.2 Gb (2.74-3.67 Gb) (based on two species, Eupyrmna scolopes and Doryteuthis pleii) GoaT (genomehubs.org).

Due to the rarity of samples, we will require the supplier to duplicate extraction of DNA, testing of DNA quality/quantity and genotype-by-sequencing per sample. All samples have been obtained and are ready to be sent as soon as the Contract is finalised.

Deliverables:
• DNA Quality Control report (i.e. pass/fail based on DNA concentration and DNA quality) supplied to Cefas before genotype-by-sequencing commences.
• Genotype-by-sequencing providing SNPS with an average of 30x depth.
• Quality control report of genotype-by-sequencing to ensure desired coverage.
• Sequencing files to be provided in compressed fastq format.
• All results must be received by 1st December 2024.
; Download the Bidder Pack at https://defra-family.force.com/s/Welcome and search for CEFAS24-126 under opportunities.