Malus x domestica WA 38 Genome v1.0 Assembly & Annotation
Overview
Publication: Zhang, H., Ko, I., Eaker, A., Haney, S., Khuu, N., Ryan, K., Appleby, A. B., Hoffmann, B., Landis, H., Pierro, K. A., Willsea, N., Hargarten, H., Yocca, A. E., Harkess, A., Honaas, L., & Ficklin, S. (2024). A haplotype-resolved, chromosome-scale genome for Malus domestica Borkh. ‘WA 38’. G3: Genes|Genomes|Genetics. https://doi.org/10.1093/g3journal/jkae222
Statistics of Genome Assembly
Homology
Homology of the Malus x domestica WA 38 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 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format. Protein Homologs
Assembly
The Malus x domestica WA 38 Genome v1.0 assembly files are available in FASTA format. Downloads
Gene Predictions
The Malus x domestica WA 38 v1.0.a1 genome gene prediction file are available in GFF3 and FASTA format. Downloads
Functional Analysis
Functional annotation for the Malus x domestica WA 38 genome v1.0 are available for download below. The Malus x domestica WA 38 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).
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 Malus x domestica WA 38 genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.
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