| Analysis Name | Malus baccata v1.0 Assembly & Annotation |
| Sequencing technology | Illumina HiSeq |
| Assembly method | SOAPdenovo v. 2.04.4; SSPACE v. 2.0; GapCloser v. 1.10 |
| Release Date | 2019-07-03 |
Chen X, Li S, Zhang D, Han M, Jin X, Zhao C, Wang S, Xing L, Ma J, Ji J, An N. Sequencing of a Wild Apple (Malus baccata) Genome Unravels the Differences Between Cultivated and Wild Apple Species Regarding Disease Resistance and Cold Tolerance. G3 (Bethesda). 2019 Jul 9;9(7):2051-2060. doi: 10.1534/g3.119.400245.
AbstractMalus baccata is one of four wild apple species that can hybridize with the cultivated apple species (Malus domestica). It is widely used in high-latitude apple-producing areas as a rootstock and breeding resource because of its disease resistance, and cold tolerance. A lack of a reference genome has limited the application of M. baccata for apple breeding. We present a draft reference genome for M. baccata. The assembled sequence consisting of 665 Mb, with a scaffold N50 value of 452 kb, included transposable elements (413 Mb) and 46,114 high-quality protein-coding genes. According to a genetic map derived from 390 sibling lines, 72% of the assembly and 85% of the putative genes were anchored to 17 linkage groups. Many of the M. baccata genes under positive selection pressure were associated with plant–pathogen interaction pathways. We identified 2,345 Transcription factor-encoding genes in 58 families in the M. baccata genome. Genes related to disease defense and cold tolerance were also identified. A total of 462 putative nucleotide-binding site (NBS)-leucine-rich-repeat (LRR) genes, 177 Receptor-like kinase (RLK) and 51 receptor-like proteins (RLP) genes were identified in this genome assembly. The M. baccata genome contained 3978 cold-regulated genes, and 50% of these gene promoter containing DREB motif which can be induced by CBF gene. We herein present the first M. baccata genome assembly, which may be useful for exploring genetic variations in diverse apple germplasm, and for facilitating marker-assisted breeding of new apple cultivars exhibiting resistance to disease and cold stress.
Assembly statistics
| Genome size | 674.4 Mb |
| Total ungapped length | 624.8 Mb |
| Number of scaffolds | 47,473 |
| Scaffold N50 | 481.8 kb |
| Scaffold L50 | 389 |
| Number of contigs | 68,524 |
| Contig N50 | 54.7 kb |
| Contig L50 | 3,250 |
| GC percent | 38 |
| Genome coverage | 248.0x |
| Assembly level | Scaffold |
The Malus baccata v1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Malus_baccata_v1.0.fasta.gz |
The Malus baccata v1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Malus_baccata_v1.0.gff.gz |
| CDS sequences (FASTA file) | Malus_baccata_v1.0_cds.fasta.gz |
| Protein sequences (FASTA file) | Malus_baccata_v1.0_pep.fasta.gz |
Functional annotation for the Malus baccata v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Malus_baccata_Genome_v1.0.Pfam.tsv.gz |
Malus S genes Nucleotide
Malus S genes Protein