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

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 availabl...

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Detalles Bibliográficos
Autores principales: Poisson, William, Prunier, Julien, Carrier, Alexandra, Gilbert, Isabelle, Mastromonaco, Gabriela, Albert, Vicky, Taillon, Joëlle, Bourret, Vincent, Droit, Arnaud, Côté, Steeve D., Robert, Claude
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10037892/
https://www.ncbi.nlm.nih.gov/pubmed/36959567
http://dx.doi.org/10.1186/s12864-023-09189-5
Descripción
Sumario: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 comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids. CONCLUSIONS: Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09189-5.