| Analysis Name | Malus x domestica HFTH1 Assembly & Annotation |
| Sequencing technology | Illumina PE, Pacific Biosciences SMRT |
| Assembly method | Falcon45 (v0.4) |
| Release Date | 2019-04-09 |
Zhang L, Hu J, Han X, Li J, Gao Y, Richards CM, Zhang C, Tian Y, Liu G, Gul H, Wang D, Tian Y, Yang C, Meng M, Yuan G, Kang G, Wu Y, Wang K, Zhang H, Wang D, Cong P. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat Commun. 2019 Apr 2;10(1):1494. doi: 10.1038/s41467-019-09518-x.
AbstractA complete and accurate genome sequence provides a fundamental tool for functional genomics and DNA-informed breeding. Here, we assemble a high-quality genome (contig N50 of 6.99 Mb) of the apple anther-derived homozygous line HFTH1, including 22 telomere sequences, using a combination of PacBio single-molecule real-time (SMRT) sequencing, chromosome conformation capture (Hi-C) sequencing, and optical mapping. In comparison to the Golden Delicious reference genome, we identify 18,047 deletions, 12,101 insertions and 14 large inversions. We reveal that these extensive genomic variations are largely attributable to activity of transposable elements. Interestingly, we find that a long terminal repeat (LTR) retrotransposon insertion upstream of MdMYB1, a core transcriptional activator of anthocyanin biosynthesis, is associated with red-skinned phenotype. This finding provides insights into the molecular mechanisms underlying red fruit coloration, and highlights the utility of this high-quality genome assembly in deciphering agriculturally important trait in apple.
Assembly statistics
| Sequence coverage (×) | 183 |
| Sequenced genome size (Mb) | 660.5 |
| Contig Number | 502 |
| Contig N50 (Mb) | 6.99 |
The Malus x domestica HFTH1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | HFTH1.all.chr.fa.gz |
The Malus x domestica HFTH1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | HFTH1.gene.gff3.gz |
| CDS sequences (FASTA file) | HFTH1.gene.cds.fa.gz |
| Protein sequences (FASTA file) | HFTH1.gene.pep.fa.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | Domain |
| MdSFBB.XVI-S9 | Chr 17 | 33998825 | 29860443-29861630 | F-box; F_box_assoc |
| MdSFBB.XVII-S9 | Chr 17 | 33998825 | 29880819-29879614 | F-box; F_box_assoc |
| MdSFBB.XIV-S9 | Chr 17 | 33998825 | 29883107-29884312 | F-box; F_box_assoc |
| MdSFBB.Ib-S9 | Chr 17 | 33998825 | 29943756-29942554 | F-box; F_box_assoc |
| MdSFBB.VI-S9 | Chr 17 | 33998825 | 29999810-29998632 | F-box; F_box_assoc |
| MdSFBB.III-S9 | Chr 17 | 33998825 | 30121504-30122685 | F-box; F_box_assoc |
| MdSFBB.II-S9 | Chr 17 | 33998825 | 30224230-30225423 | F-box; F_box_assoc |
| MdSFBB.IV-S9 | Chr 17 | 33998825 | 30236989-30238173 | F-box; F_box_assoc |
| MdSFBB.XV-S9 | Chr 17 | 33998825 | 30289634-30290848 | F-box; F_box_assoc |
| MdSFBB.Ia-S9 | Chr 17 | 33998825 | 30392432-30393634 | F-box; F_box_assoc |
| MdSFBB.X-S9 | Chr 17 | 33998825 | 30477857-30476676 | F-box; F_box_assoc |
| MdSFBB.XI-S9 | Chr 17 | 33998825 | 30520884-30519700 | F-box; F_box_assoc |
| MdSFBB.XII-S9 | Chr 17 | 33998825 | 30649328-30648156 | F-box; F_box_assoc |
| MdSFBB.XVIII-S9 | Chr 17 | 33998825 | 30716312-30715128 | F-box; F_box_assoc |
| MdSFBB.VII-S9 | Chr 17 | 33998825 | 30787708-30786530 | F-box; F_box_assoc |
| S9-RNase | Chr 17 | 33998825 | 30891703-30891452,30891307-30890873 | RNase_T2 |
| MdSFBB.V-S9 | Chr 17 | 33998825 | 30933865-30935043 | F-box; F_box_assoc |
| MdSFBB.VIII.2-S9 | Chr 17 | 33998825 | 31068766-31067573 | F-box; F_box_assoc |
| MdSFBB.VIII.1-S9 | Chr 17 | 33998825 | 31116911-31115721 | F-box; F_box_assoc |
| MdSFBB.XXI-S9 | Chr 17 | 33998825 | 31827099-31828448 | F-box; F_box_assoc |
Malus x domestica HFTH1 S genes Nucleotide
Malus x domestica HFTH1 S genes Protein