The Rodent 2K consortium includes rodent researchers, field biologists, bioinformaticians and conservation organisationw such as national history museums to sequence the genomes of the approximatively 2500 known living rodent species. Understanding the DNA sequence variation amongst all rodents will enable us to uncover genetic mechanisms leading to their unusual traits and adaptation to extreme environment on earth. This large genomic resource will also provide an evolutionary context to better understand the mouse genome which is the most used model organism for biomedical research.
It is now possible to sequence and assemble the genome of a mammalian species for a few thousand dollars, within a few days and with a quality and completeness that surpasses the first generated human assembly. This makes it possible to sequence at scale the genomes of rodents to uncover traits with biomedical applications such as tissue regeneration, cancer resistance, pain insensitivity, water efficiency and more. This will also provide precious data on rodent biodiversity that will be put at the disposal of conservation efforts.
General strategy
The Rodent 2K project aims to produce high quality and usable rodent genome assemblies. This means that genomes will be sequenced and assembled with a minimum contigs N50 of 1 Mb and at the chromosome level. Genome annotation and multiple whole genome alignments will be produced to enable genomic and comparative genomic analyses by the community.
The project consists of different stages:
Stage 0 This stage is now complete, and was the proof of concept and led to the sequencing and assembly of several rodent species at the chromosome level. This stage main goal was to develop connections amongst rodent researchers, field biologists and bioinformaticians with the required expertise to initiate the consortium.
Stage 1 The 63 rodent sub families will be targeted to have at least one representative per subfamily .
Stage 2 The remaining 430 genera will be targeted to have at least to have at least one representative per subfamily.
Stage 3 All other rodent species will be sequenced.