Prunus avium Regina Genome v1.0 Assembly & Annotation
Overview
Data Source: https://doi.org/10.15454/KEW474 Description This dataset includes the preliminary assembly and structural annotation of the version 1 (V1) of 'Regina' sweet cherry genome, following genome sequencing using PacBio long reads and optical mapping. We have reconstructed the pseudomolecules at near chromosome level using high density genetic linkage maps with GBS data. (2020-05-11) Related Publication Le Dantec L, Girollet N, Gouzy J, Sallet E, Fouché M, Quero-Garcia J, Dirlewanger E (2019) An Improved Assembly of the Diploid ‘Regina’ Sweet Cherry Genome. International Plant & Animal Genome XXVII / January 12-16, 2019 - San Diego, CA, USA.
Homology
Homology of the Prunus avium Regina 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 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. Protein Homologs
Assembly
The Prunus avium Regina genome v1.0 assembly file is available in FASTA format. Downloads
Gene Predictions
The Prunus avium Regina genome v1.0 gene prediction files are available in GFF3 and FASTA format. Downloads
Functional Analysis
Functional annotation for the Prunus avium Regina genome v1.0 are available for download below. The Prunus avium Regina 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 Prunus avium Regina genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.
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