Malus x domestica 'M9' Whole Genome v1.0.a2 Assembly & Annotation
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Overview
Publication Li, W., Chu, C., Li, H. et al. Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing. Nat Genet (2024) https://doi.org/10.1038/s41588-024-01657-2 Description Dwarfing rootstocks have transformed the production of cultivated apples; however, the genetic basis of rootstock-induced dwarfing remains largely unclear. We have assembled chromosome-level, near-gapless and haplotype-resolved genomes for the popular dwarfing rootstock ‘M9’, the semi-vigorous rootstock ‘MM106’ and ‘Fuji’, one of the most commonly grown apple cultivars. The apple orthologue of auxin response factor 3 (MdARF3) is in the Dw1 region of ‘M9’, the major locus for rootstock-induced dwarfing. Comparing ‘M9’ and ‘MM106’ genomes revealed a 9,723-bp allele-specific long terminal repeat retrotransposon/gypsy insertion, DwTE, located upstream of MdARF3. DwTE is cosegregated with the dwarfing trait in two segregating populations, suggesting its prospective utility in future dwarfing rootstock breeding. In addition, our pipeline discovered mobile mRNAs that may contribute to the development of dwarfed scion architecture. Our research provides valuable genomic resources and applicable methodology, which have the potential to accelerate breeding dwarfing rootstocks for apple and other perennial woody fruit trees. Annotation of Whole Genome Assembly
Statistics of Genome Assembly
Homology
Homology of the Malus x domestica M9 genome v1.0.a2 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 Malus x domestica M9 Genome v1.0.a2 assembly files are available in FASTA format. Downloads
Gene Predictions
The Malus x domestica M9 v1.0.a2 genome gene prediction files are available in GFF3 and FASTA format. Downloads
Functional Analysis
Functional annotations for the Malus x domestica M9 genome v1.0.a2 are available for download below. The Malus x domestica M9 genome v1.0.a2 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 domesticaM9 genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.
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