Table 1.
Filtered Oxford Nanopore reads used for the ‘Malling Jewel’ and ‘Autumn Bliss’ genome sequence assemblies.
Table 2.
Assembly statistics for the de novo assemblies of the Rubus idaeus ‘Malling Jewel’ and ‘Autumn Bliss’ genome sequences.
Table 3.
Rubus idaeus ‘Malling Jewel’ and ‘Autumn Bliss’ contigs aligning to ‘Anitra’ genome pseudomolecules.
Table 4.
Assembly statistics for the reference scaffolded assemblies of the Rubus idaeus ‘Anitra’, ‘Malling Jewel’ and ‘Autumn Bliss’ genome sequences.
Fig 1.
The red raspberry genome assemblies of ‘Autumn Bliss’ and ‘Malling Jewel’ show synteny to the previously published ‘Anitra’ genome.
The dot plots show the alignments of ‘Autumn Bliss’ and ‘Malling Jewel’ genome assemblies to the ‘Anitra’ genome sequence. The plots show the synteny between ‘Autumn Bliss’ and ‘Malling Jewel’ contigs (y-axis) aligning to the ‘Anitra’ pseudochromosomes (x-axis). ‘Anitra’ chromosome names are given along with total assembly lengths of the ‘Anitra’, ‘Autumn Bliss (a) and ‘Malling Jewel’ (b) chromosomes in Mbp. The hashed horizontal lines indicate the positions along the y-axis of the assembled scaffolds in each assembly. ‘Autumn Bliss’ and ‘Malling Jewel’ scaffold names and sizes are given in S2 Fig.
Fig 2.
Extensive repetitive regions were identified throughout the pseudochromosomes of the ‘Anitra’, ‘Autumn Bliss’ and ‘Malling Jewel’ genome sequence assemblies.
Circos plots showing the distribution of coding regions (green) and repetitive regions (red) in the ‘Autumn Bliss’, ‘Malling Jewel’ and ‘Anitra’ genome sequence assemblies along with the alignment of syntenic regions of ‘Autumn Bliss’ and ‘Malling Jewel’ to the ‘Anitra’ genome. Major tick marks indicate 5 Mb intervals and minor ticks indicate 1 Mb intervals.
Fig 3.
The density of repetitive sequences in the ‘Autumn Bliss’ and ‘Malling Jewel’ genome assemblies was substantially higher than in the previously published ‘Anitra’ assembly.
Bar charts displaying the number of tandem repeat regions and total repetitive regions identified per chromosome in the ‘Anitra’, ‘Autumn Bliss’ and ‘Malling Jewel’ genomes using Tandem Repeat Finder.
Table 5.
A comparison of Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis of the proteome from the previously published ‘Anitra’ genome, the reannotated ‘Anitra’ genome, ‘Malling Jewel’ and ‘Autumn Bliss’.
Table 6.
Summary statistics for the number of protein-coding gene predictions for ‘Anitra’, ‘Autumn Bliss’ and ‘Malling Jewel’ that returned ≥1 positive hit after the BlastP analysis with nr, Araport11, RefSeq, SwissProt and TrEMBL databases as subjects, along with the number of protein-coding gene regions assigned Interpro, GO, KEGG orthology and KEGG pathway terms.
Fig 4.
A Venn diagram showing the distribution of the 5,286 Rubus idaeus-specific orthogroups identified in this study between the ‘Anitra’, ‘Autumn Bliss’ and ‘Malling Jewel’ genomes.
Fig 5.
Overrepresented Gene Ontology (GO) categories in the orthogroups shared across ‘Anitra’, ‘Autumn Bliss’ and ‘Malling Jewel’ cultivars highlight key conserved processes.
The circles are shaded based on significance level (yellow = False Discovery Rate (FDR) below 5.00E-2), and the radius of circles is proportional to the number of orthogroups included in each GO category.