Rubus argutus Hillquist Genome v1.0 Assembly & Annotation

Analysis NameRubus argutus Hillquist Genome v1.0 Assembly & Annotation
MethodFALCON, Juicer
SourcePacBio, Hi-C, 10x Genomics (Rubus argutus PI 553951)
Date performed2022-04-20

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 Link., cv. ‘Hillquist’).  Submitted. Preprint bioRxiv

Data use before publication:  The authors have kindly provided this data pre-publication according to the Ft. Lauderdale Accord. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by the authors and/or collaborators of a comprehensive genome analysis such as identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome-scale comparisons with other species. 


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

Rubus argutus v1.0 proteins with NCBI nr homologs (EXCEL file) Rargutus_Hillquist_v1.0_vs_nr.xlsx.gz
Rubus argutus v1.0 proteins with NCBI nr (FASTA file) Rargutus_Hillquist_v1.0_vs_nr_hit.fasta.gz
Rubus argutus v1.0 proteins without NCBI nr (FASTA file) Rargutus_Hillquist_v1.0_vs_nr_noHit.fasta.gz
Rubus argutus v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Rargutus_Hillquist_v1.0_vs_arabidopsis.xlsx.gz
Rubus argutus v1.0 proteins with arabidopsis (Araport11) (FASTA file) Rargutus_Hillquist_v1.0_vs_arabidopsis_hit.fasta.gz
Rubus argutus v1.0 proteins without arabidopsis (Araport11) (FASTA file) Rargutus_Hillquist_v1.0_vs_arabidopsis_noHit.fasta.gz
Rubus argutus v1.0 proteins with SwissProt homologs (EXCEL file) Rargutus_Hillquist_v1.0_vs_swissprot.xlsx.gz
Rubus argutus v1.0 proteins with SwissProt (FASTA file) Rargutus_Hillquist_v1.0_vs_swissprot_hit.fasta.gz
Rubus argutus v1.0 proteins without SwissProt (FASTA file) Rargutus_Hillquist_v1.0_vs_swissprot_noHit.fasta.gz
Rubus argutus v1.0 proteins with TrEMBL homologs (EXCEL file) Rargutus_Hillquist_v1.0_vs_trembl.xlsx.gz
Rubus argutus v1.0 proteins with TrEMBL (FASTA file) Rargutus_Hillquist_v1.0_vs_trembl_hit.fasta.gz
Rubus argutus v1.0 proteins without TrEMBL (FASTA file) Rargutus_Hillquist_v1.0_vs_trembl_noHit.fasta.gz



The Rubus argutus Hillquist Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) Rargutus_Hillquist_v1.0.fasta.gz


Gene Predictions

The Rubus argutus Hillquist Genome v1.0 gene prediction files are available in FASTA and GFF3 formats.


Protein sequences  (FASTA file) Rargutus_Hillquist_v1.0.proteins.fasta.gz
Genes (GFF3 file) Rargutus_Hillquist_v1.0.genes.gff3.gz


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).


GO assignments from InterProScan Rargutus_Hillquist_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Rargutus_Hillquist_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Rargutus_Hillquist_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Rargutus_Hillquist_v1.0_KEGG-pathways.xlsx.gz


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.


Fragaria x ananassa GDR RefTrans v1 Rargutus_Hillquist_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 Rargutus_Hillquist_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Rargutus_Hillquist_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Rargutus_Hillquist_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Rargutus_Hillquist_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Rargutus_Hillquist_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Rargutus_Hillquist_v1.0_pyrus_GDR_reftransV1