Malus x domestica ‘Honeycrisp’ Genome v1.1.a1 Assembly & Annotation
Overview
Publication: Awais Khan, Sarah B. Carey, Alicia Serrano, Huiting Zhang, Heidi Hargarten, Haley Hale, Alex Harkess, Loren Honaas, A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica),Gigabyte,2022 https://doi.org/10.46471/gigabyte.69 (GDR | Journal) Abstract: The apple cultivar ‘Honeycrisp’ has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent. However, it suffers from several physiological disorders, production, and postharvest issues. Despite several available apple genome sequences, understanding of the genetic mechanisms underlying cultivar-specific traits remains lacking. Here, we present a highly contiguous, fully phased, chromosome-level genome of ‘Honeycrisp’ apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms, with two assembled haplomes of 674 Mbp and 660 Mbp, and contig N50 values of 32.8 Mbp and 31.6 Mbp, respectively. Overall, 47,563 and 48,655 protein-coding genes were annotated from each haplome, capturing 96.8–97.4% complete BUSCOs in the eudicot database. Gene family analysis reveals most ‘Honeycrisp’ genes are assigned into orthogroups shared with other genomes, with 121 ‘Honeycrisp’-specific orthogroups. This resource is valuable for understanding the genetic basis of important traits in apples and related Rosaceae species to enhance breeding efforts. Summary of ‘Honeycrisp’ genome assembly statistics
Homology
Homology of the Malus x domestica Honeycrisp 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 Malus x domestica Honeycrisp Genome v1.1 assembly files are available in FASTA format. Downloads
Gene Predictions
The Malus x domestica Honeycrisp v1.1 genome gene prediction files are available in GFF3 and FASTA format. Downloads
Functional Analysis
Functional annotation for the Malus x domestica Honeycrisp Genome v1.0 are available for download below. The Malus x domestica Honeycrisp 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 Malus x domestica Honeycrisp 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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