Rubus argutus Hillquist Genome v1.0 Assembly & Annotation
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Overview
Accession number: tfGDR1056 Publication: Bruna T, Aryal R, Dudchenko O, Sargent DJ, Mead D, Buti M, Cavallini A, Hytonen T, Andres J, Pham M, Weisz D, Mascagni F, Usai G, Natali L, Bassil N, Fernandez GE, Lomsadze A, Armour M, Olukolu B, Poorten T, Britton C, Davik J, Ashrafi H, Aiden EL, Borodovsky M, Worthington M. 2022. A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. ‘Hillquist’). G3 Genes|Genomes|Genetics, jkac289, https://doi.org/10.1093/g3journal/jkac289 Homology
Homology of the Rubus argutus Hillquist 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-9 was used for the NCBI nr (Release 2021-09) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.
Protein Homologs
Assembly
The Rubus argutus Hillquist Genome v1.0 assembly file is available in FASTA format. Downloads
Gene Predictions
The Rubus argutus Hillquist Genome v1.0 gene prediction files are available in FASTA and GFF3 formats. Downloads
Functional Analysis
Functional annotation for the Rubus argutus Hillquist Genome v1.0 are available for download below. The Rubus argutus 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 argutus 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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