A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.).
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2022
2022
Historique:
received:
29
11
2021
accepted:
22
02
2022
entrez:
16
3
2022
pubmed:
17
3
2022
medline:
4
5
2022
Statut:
epublish
Résumé
Rubus idaeus L. (red raspberry), is a perennial woody plant species of the Rosaceae family that is widely cultivated in the temperate regions of world and is thus an economically important soft fruit species. It is prized for its flavour and aroma, as well as a high content of healthful compounds such as vitamins and antioxidants. Breeding programs exist globally for red raspberry, but variety development is a long and challenging process. Genomic and molecular tools for red raspberry are valuable resources for breeding. Here, a chromosome-length genome sequence assembly and related gene predictions for the red raspberry cultivar 'Anitra' are presented, comprising PacBio long read sequencing scaffolded using Hi-C sequence data. The assembled genome sequence totalled 291.7 Mbp, with 247.5 Mbp (84.8%) incorporated into seven sequencing scaffolds with an average length of 35.4 Mbp. A total of 39,448 protein-coding genes were predicted, 75% of which were functionally annotated. The seven chromosome scaffolds were anchored to a previously published genetic linkage map with a high degree of synteny and comparisons to genomes of closely related species within the Rosoideae revealed chromosome-scale rearrangements that have occurred over relatively short evolutionary periods. A chromosome-level genomic sequence of R. idaeus will be a valuable resource for the knowledge of its genome structure and function in red raspberry and will be a useful and important resource for researchers and plant breeders.
Identifiants
pubmed: 35294470
doi: 10.1371/journal.pone.0265096
pii: PONE-D-21-37284
pmc: PMC8926247
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0265096Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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