Rubus idaeus cv. 'Autumn Bliss' NIAB Genome v1.0 Assembly & Annotation
Overview
Publication Price, R. J., Davik, J., Fernandéz Fernandéz, F., Bates, H. J., Lynn, S., Nellist, C. F., Buti, M., Røen, D., Šurbanovski, N., Alsheikh, M., Harrison, R. J., & Sargent, D. J. (2023). Chromosome-scale genome sequence assemblies of the ‘Autumn Bliss’ and ‘Malling Jewel’ cultivars of the highly heterozygous red raspberry (Rubus idaeus L.) derived from long-read Oxford Nanopore sequence data. PLoS ONE, 18(5), e0285756. https://doi.org/10.1371/journal.pone.0285756. Abstract Table 2. Assembly statistics for the de novo assemblies of the Rubus idaeus ‘Malling Jewel’ and ‘Autumn Bliss’ genome sequences.
Homology
Homology of the Rubus idaeus 'Autumn Bliss' genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-6 for the Arabidoposis proteins (Araport11 2022-09), UniProtKB/SwissProt (Release 2023-06), and UniProtKB/TrEMBL (Release 2023-06) databases. The best hit reports are available for download in Excel format.
Protein Homologs
Assembly
The Rubus idaeus 'Autumn Bliss' NIAB Genome v1.0 assembly file is available in FASTA format. Downloads
Gene Predictions
The Rubus idaeus 'Autumn Bliss' NIAB V1.0 genome gene prediction files are available in GFF3 and FASTA format. Downloads
Functional Analysis
Functional annotation for the Rubus idaeus 'Autumn Bliss' genome v1.0 are available for download below. The Rubus idaeus Genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS). Downloads
Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Rubus idaeus Autumn Bliss genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.
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