| Analysis Name | Malus orientalis MO Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | FALCON v. 16.1 |
| Release Date | 2023-11-22 |
Wang T, Duan S, Xu C, Wang Y, Zhang X, Xu X, Chen L, Han Z, Wu T. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nat Commun. 2023 Nov 15;14(1):7377. doi: 10.1038/s41467-023-43270-7.
AbstractStructural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar 'Granny Smith' and the widely cultivated cultivar 'Red Fuji'. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs. We also observe CNVs that are positively correlated with expression levels of the genes they are associated with. Furthermore, we show that the noncoding RNA generated from a 209 bp insertion in the intron of mitogen-activated protein kinase homology encoding gene, MMK2, regulates the gene expression and affects fruit coloration. Moreover, we identify overlapping SVs associated with fruit quality and biotic resistance. This pan-genome uncovers possible contributions of CNVs to gene expression and highlights the role of SVs in apple domestication and economically important traits.
Assembly statistics
| Genome size | 664.5 Mb |
| Total ungapped length | 664 Mb |
| Number of chromosomes | 17 |
| Number of scaffolds | 198 |
| Scaffold N50 | 39 Mb |
| Scaffold L50 | 8 |
| Number of contigs | 471 |
| Contig N50 | 33.3 Mb |
| Contig L50 | 9 |
| GC percent | 38 |
| Genome coverage | 30.0x |
| Assembly level | Chromosome |
The Malus orientalis MO Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_033883245.1_MO_genomic.fna.gz |
The Malus orientalis MO genome gene prediction files is available in GFF3 format.
Downloads
| Genes (GFF3 file) | MA.gff.gz |
Functional annotation for the Malus orientalis MO is not available.
Downloads
| Domain from InterProScan | - |
Malus S genes Nucleotide
Malus S genes Protein