tinyurl.com
Register your interest in participating in the Global Culicidae Reference Genomes Project
We are seeking mosquito biologists around the world who would be interested in collecting and contributing specimens of any vector species that currently lacks a reference genome.
Aim: We are aiming to complete a pilot project to build highly complete and contiguous long-read assemblies for 100 described mosquito species that currently lack reference genomes to remedy fundamental gaps in vector control. Our ultimate aim will be to complete reference genomes for all 3500+ described Culicidae species but that will require large-scale funding. We are completing this pilot project to demonstrate feasibility and value before seeking such funding.
Data Generation: This pilot project will aim to construct a high quality reference genome for each species using 30x coverage PacBio HiFi data and 50x coverage Hi-C data from a single specimen. However, two specimens may be required to obtain sufficient data for some species, e.g. those with small bodies and/or large genomes. As the project progresses, we may also generate long-read data using Oxford Nanopore Technologies (ONT).
Once data are generated and an assembly is completed, the assembly will go through genome curation. Upon curation completion, the raw data, the resulting assembly, and all associated collection metadata will be released to ENA for immediate use for any purpose. Each assembly will also be published as a "genome note" with the primary collector(s) listed as the first author (e.g. see https://wellcomeopenresearch.org/treeoflife ).
Number and sex of mosquito specimens requested: We ask for at least 5–10 mosquitoes per species because challenges may arise with species identification and obtaining sufficient material. Either or both sexes is fine. We cannot accept DNA.
How to preserve specimens: Mosquitoes need to be collected alive, and ideally snap frozen, or put into a suitable preservation solution immediately upon live collection. Desiccated or long-term stored specimens are unlikely to result in the quality and quantity of DNA needed.
For species that lack RNA-sequencing data, providing additional male and female specimens in an RNA preservative (such as RNALater) is requested so that RNA-seq data can be generated and used for annotations.
It is possible to ship specimens without cold-chain, and further details on how to do this will be shared with you if your species is selected for the pilot, however it is best practice to keep specimens at -80°C from collection until shipment.
Target species:. Please note that as part of other projects, we have already produced high quality genomes for multiple Anopheles species (see https://www.ebi.ac.uk/ena/browser/view/PRJEB51690), Culex pipiens, and Sabethes cyaneus. We are seeking species that currently lack reference genomes and where there is a research and/or vector control community that will benefit from filling this gap. Our top priority is known vector species that are implicated in disease transmission to humans or livestock. We will also accept species closely related to known vectors if there is good scientific motivation. If there is a compelling case to generate a reference genome for a species that already has one available, please explain why this is needed. Due to regulatory burden (as explained below) we will likely prioritize contributions from participants who are able to contribute 5+ species.
Next steps: If you are interested in contributing one or more Culicidae species to this pilot, please register your interest by filling in this survey as completely as you can.
Please be aware that multiple steps must be completed before we will be able to receive any specimens. The process typically involves an MTA (or a donation form), the completion of ABS or Nagoya compliance (this can be a lengthy process), and training on the metadata entry required for reference genomes as well as the preservation and shipment approaches. If the species you propose are accepted into the pilot, you will need to complete these steps, and only once they are complete will we be able to accept your specimens. Once specimens have been received, it may take up to 12 months for the genome to be completed and released if everything goes smoothly.
Please be aware that due to the burden of these required steps, we will likely prioritise proposals from participants who are able to contribute 5+ species and where the material is likely to be successful.
Other important information:
All sequencing costs will be covered by the pilot project, but unfortunately we do not have funds to support mosquito collections. We ask that you cover the cost of shipment to the UK (at room temperature) but if you are unable to do so, we may be able to cover these costs.
This form asks for your email address, which we will need to get in touch with you. So please enter the email address where we can reliably reach you. We will not share it with anyone else.
We will monitor responses to this survey on a weekly basis and we will be in touch with you within a couple weeks either to invite you for a brief call if your proposal meets the criteria above, or to inform you that at this stage, we are not prepared to move your proposal forward.
Thank you for your interest.
Mara Lawniczak - Wellcome Sanger Institute
Miguel Antonio Garcia Knight - National Autonomous University of Mexico & Wellcome Sanger Institute
Bernard Kim - Princeton University
Lindy McBride - Princeton University
