| Analysis Name | Malus sieversii Haploid Consensus Whole Genome v1.0 Assembly & Annotation |
| Sequencing technology | Illumina and PacBio HiFi reads |
| Assembly method | DeNovoMAGIC3, Hifiasm and HiCanu |
| Release Date | 2021-04-21 |
Sun X, Jiao C, Schwaninger H, Chao CT, Ma Y, Duan N, Khan A, Ban S, Xu K, Cheng L, Zhong GY, Fei Z. Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat Genet. 2020 Dec;52(12):1423-1432. doi: 10.1038/s41588-020-00723-9.
AbstractDomestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.
The Malus sieversii Haploid Consensus Whole Genome v1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | Msieversii_Haploid_v2.chr.fa.gz |
The Malus sieversii Haploid Consensus Whole Genome v1.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Msieversii_Haploid_v2.gff.gz |
| CDS sequences (FASTA file) | Msieversii_Haploid_v2.cds.fa.gz |
| Protein sequences (FASTA file) | Msieversii_Haploid_v2.pep.fa.gz |
Functional annotation for the Malus sieversii Haploid Consensus Whole Genome v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Malus_sieversii_Haploid_Consensus_Whole_Genome_v1.0.Pfam.tsv.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | BLASTn Hit | BLASTn %ID | Domain |
| SFBB.XVI | chr17 | 34175717 | 30253730-30254917 | MdSFBB.XVI-S9 | 99.16 | F-box; F_box_assoc |
| SFBB.XVII | chr17 | 34175717 | 30272304-30271120 | MdSFBB.XVII-S9 | 99.34 | F-box; F_box_assoc |
| SFBB.XIV | chr17 | 34175717 | 30280244-30281449 | MdSFBB.XIV-S9 | 99.337 | F-box; F_box_assoc |
| SFBB.Ib | chr17 | 34175717 | 30344587-30343385 | MdSFBB.Ib-S9 | 99.584 | F-box; F_box_assoc |
| SFBB.VI | chr17 | 34175717 | 30373546-30372368 | MdSFBB.VI-S9 | 98.982 | F-box; F_box_assoc |
| SFBB.III | chr17 | 34175717 | 30464606-30465787 | MdSFBB.III-S9 | 98.562 | F-box; F_box_assoc |
| SFBB.II | chr17 | 34175717 | 30489885-30491078 | MdSFBB.II-S9 | 97.069 | F-box; F_box_assoc |
| SFBB.IV | chr17 | 34175717 | 30494902-30496083 | MdSFBB.IV-S9 | 97.295 | F-box; F_box_assoc |
| SFBB.XV | chr17 | 34175717 | 30630637-30631851 | MdSFBB.XV-S9 | 96.379 | F-box; F_box_assoc |
| SFBB.Ia | chr17 | 34175717 | 30692938-30694140 | MdSFBB.Ia-S9 | 97.074 | F-box; F_box_assoc |
| SFBB.X | chr17 | 34175717 | 30730231-30729050 | MdSFBB.X-S9 | 96.616 | F-box; F_box_assoc |
| SFBB.XI | chr17 | 34175717 | 30799315-30798131 | MdSFBB.XI-S9 | 95.949 | F-box; F_box_assoc |
| SFBB.XII | chr17 | 34175717 | 30974975-30976150 | MdSFBB.XII-S9 | 93.452 | F-box; F_box_assoc |
| SFBB.Ic | chr17 | 34175717 | 31010821-31012017 | MdSFBB.Ia-S9 | 88.226 | F-box; F_box_assoc |
| SFBB.V | chr17 | 34175717 | 31165357-31164179 | MdSFBB.V-S9 | 92.791 | F-box; F_box_assoc |
| SFBB.VII | chr17 | 34175717 | 31229757-31228579 | MdSFBB.VII-S9 | 95.505 | F-box; F_box_assoc |
| SFBB.XIX | chr17 | 34175717 | 31346123-31344927 | ON918629.1, PbrSFBB.XIX-S17 | 96.353 | F-box; F_box_assoc |
| SFBB.XVIII | chr17 | 34175717 | 31364895-31363711 | MdSFBB.XVIII-S9 | 96.203 | F-box; F_box_assoc |
| SFBB.VIII | chr17 | 34175717 | 31421186-31419996 | MdSFBB.VIII.1-S9 | 98.237 | F-box; F_box_assoc |
| SFBB.XXI | chr17 | 34175717 | 32077026-32078375 | MdSFBB.XXI-S9 | 99.481 | F-box; F_box_assoc |
| S-RNase | chr17 | 34175717 | 31078114-31077872,31077527-31077090 | MG598487.1, S1-RNase | 100 | RNase_T2 |
Malus sieversii Haploid_Consensus_Whole_Genome_v1.0 S genes Nucleotide
Malus sieversii Haploid_Consensus_Whole_Genome_v1.0 S genes Protein