Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.
BMC Genomics
; 24(1): 142, 2023 Mar 23.
Article
em En
| MEDLINE
| ID: mdl-36959567
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 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.Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Cervos
/
Rena
Limite:
Animals
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article