Rubus idaeus Anitra Genome v1.0 Assembly & Annotation

Overview
Analysis NameRubus idaeus Anitra Genome v1.0 Assembly & Annotation
MethodCanu
SourcePacBio
Date performed2022-03-23

Publication

Davik J, Røen D, Lysøe E, Buti M, Rossman S, Alsheikh M, Aiden EL, Dudchenko O, Sargent DJ. A chromosome-level genome sequence assembly of the red raspberry (Rubus idaeus L.).. PloS one. 2022; 17(3):e0265096.

Abstract

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.

Assembly

The Rubus idaeus Anitra Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Ridaeus_Anitra_v1.0.fasta.gz

 

Gene Predictions

The Rubus idaeus Anitra v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Ridaeus_Anitra_v1.0.proteins.fasta.gz
Genes (GFF3 file) Ridaeus_Anitra_v1.0.genes.gff3.gz