Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights ...

• Main Authors: Poisson, William, Prunier, Julien, Carrier, Alexandra, Gilbert, Isabelle, Mastromonaco, Gabriela, Albert, Vicky, Taillon, Joëlle, Bourret, Vincent, Droit, Arnaud, Côté, Steeve D., Robert, Claude
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: figshare 2023
• Subjects: Genetics; FOS Biological sciences; Rangifer tarandus
• Online Access: https://dx.doi.org/10.6084/m9.figshare.c.6593650; https://springernature.figshare.com/collections/Chromosome-level_assembly_of_the_Rangifer_tarandus_genome_and_validation_of_cervid_and_bovid_evolution_insights/6593650

Abstract Background Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. Results We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and ...