Malus fusca Genome v1.0 Assembly & Annotation
Overview
| Analysis Name | Malus fusca Genome v1.0 Assembly & Annotation |
| Sequencing technology | PacBio RSII |
| Assembly method | HiFiasm v. 0.16.1 |
| Release Date | 2024-01-12 |
Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. Plant J. 2023 Nov;116(4):989-1002. doi: 10.1111/tpj.16433.
SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation for M. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co-linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference-quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA-informed introgression breeding.
Assembly statistics
Assembly
The Malus fusca Genome v1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Mfusca_v1.0_hap1.soft.masked.fa.gz | Mfusca_v1.0_hap2.soft.masked.fa.gz |
Gene Predictions
The Malus fusca Genome v1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Mfusca_v1.0_hap1.gff.gz | Mfusca_v1.0_hap2.gff.gz |
| CDS sequences (FASTA file) | Mfusca_v1.0_hap1.CDS.fa.gz | Mfusca_v1.0_hap2.CDS.fa.gz |
| Protein sequences (FASTA file) | Mfusca_v1.0_hap1.proteins.fa.gz | Mfusca_v1.0_hap2.proteins.fa.gz |
Functional Analysis
Functional annotation for the Malus fusca Genome v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Mfusca_v1.0_hap1.Pfam.tsv.gz | Mfusca_v1.0_hap2.Pfam.tsv.gz |
S genes
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SFBB.XVI | Chr17 | 35982444 | 31946765-31947952 | MdSFBB.XVI-S9 | 99.24 | F-box; F_box_assoc |
| SFBB.XVII | Chr17 | 35982444 | 31982165-31980960 | MdSFBB.XVII-S9 | 98.92 | F-box; F_box_assoc |
| SFBB.XIV | Chr17 | 35982444 | 31984434-31985639 | MdSFBB.XIV-S9 | 99.25 | F-box; F_box_assoc |
| SFBB.Ib | Chr17 | 35982444 | 32038832-32037627 | MdSFBB.Ib-S9 | 99.25 | F-box; F_box_assoc |
| SFBB.VI | Chr17 | 35982444 | 32072753-32071575 | MdSFBB.VI-S9 | 97.54 | F-box; F_box_assoc |
| SFBB.III | Chr17 | 35982444 | 32154207-32155388 | MdSFBB.III-S9 | 98.48 | F-box; F_box_assoc |
| SFBB.II | Chr17 | 35982444 | 32204855-32206048 | MdSFBB.II-S9 | 96.7 | F-box; F_box_assoc |
| SFBB.IV | Chr17 | 35982444 | 32210333-32211517 | MdSFBB.IV-S9 | 97.63 | F-box; F_box_assoc |
| SFBB.XI | Chr17 | 35982444 | 32272707-32271522 | MdSFBB.XI-S9 | 95.87 | F-box; F_box_assoc |
| SFBB.Ia | Chr17 | 35982444 | 32391453-32392655 | MdSFBB.Ib-S9 | 94.93 | F-box; F_box_assoc |
| SFBB.Ic | Chr17 | 35982444 | 32507823-32506621 | MdSFBB.Ia-S9 | 90.61 | F-box; F_box_assoc |
| SFBB.XII | Chr17 | 35982444 | 32663508-32664686 | MdSFBB.XII-S9 | 90.09 | F-box; F_box_assoc |
| SFBB.XIb | Chr17 | 35982444 | 32771736-32770561 | MdSFBB.XI-S9 | 91.45 | F-box; F_box_assoc |
| SFBB.V | Chr17 | 35982444 | 32922201-32921023 | MdSFBB.V-S9 | 97.37 | F-box; F_box_assoc |
| SFBB.VII | Chr17 | 35982444 | 33000342-32999164 | MdSFBB.VII-S9 | 95.42 | F-box; F_box_assoc |
| SFBB.XIX | Chr17 | 35982444 | 33069853-33068621 | PbrSFBB.XIX-S17 | 97.57 | F-box; F_box_assoc |
| SFBB.XVIII | Chr17 | 35982444 | 33090986-33089802 | MdSFBB.XVIII-S9 | 95.61 | F-box; F_box_assoc |
| SFBB.VIII | Chr17 | 35982444 | 33151217-33150027 | MdSFBB.VIII.1-S9 | 97.73 | F-box; F_box_assoc |
| SFBB.XXI | Chr17 | 35982444 | 33974141-33975490 | MdSFBB.XXI-S9 | 98.74 | F-box; F_box_assoc |
| S-RNaseψ | Chr17 | 35982444 | 32679322-32679077,32678989-32678462 | MG598497.1, S11-RNase | 99.05 | - |
Malus fusca Genome_v1.0 S genes Nucleotide
- Malus fusca Genome_v1.0 SFBB.XVI mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XVII mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XIV mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.Ib mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.VI mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.III mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.II mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.IV mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XI mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.Ia mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.Ic mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XII mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XIb mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.V mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.VII mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XIX mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XVIII mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.VIII mRNA, complete cds
- Malus fusca Genome_v1.0 SFBB.XXI mRNA, complete cds
- Malus fusca Genome_v1.0 S-RNaseψ mRNA, complete cds
Malus fusca Genome_v1.0 S genes Protein
- Malus fusca Genome_v1.0 SFBB.XVI protein
- Malus fusca Genome_v1.0 SFBB.XVII protein
- Malus fusca Genome_v1.0 SFBB.XIV protein
- Malus fusca Genome_v1.0 SFBB.Ib protein
- Malus fusca Genome_v1.0 SFBB.VI protein
- Malus fusca Genome_v1.0 SFBB.III protein
- Malus fusca Genome_v1.0 SFBB.II protein
- Malus fusca Genome_v1.0 SFBB.IV protein
- Malus fusca Genome_v1.0 SFBB.XI protein
- Malus fusca Genome_v1.0 SFBB.Ia protein
- Malus fusca Genome_v1.0 SFBB.Ic protein
- Malus fusca Genome_v1.0 SFBB.XII protein
- Malus fusca Genome_v1.0 SFBB.XIb protein
- Malus fusca Genome_v1.0 SFBB.V protein
- Malus fusca Genome_v1.0 SFBB.VII protein
- Malus fusca Genome_v1.0 SFBB.XIX protein
- Malus fusca Genome_v1.0 SFBB.XVIII protein
- Malus fusca Genome_v1.0 SFBB.VIII protein
- Malus fusca Genome_v1.0 SFBB.XXI protein