| Analysis Name | Malus prunifolia Fupingqiuzi Genome v1.0 Assembly & Annotation |
| Sequencing technology | Illumina, PacBio and Hi-C |
| Assembly method | - |
| Release Date | 2022-03-29 |
Li Z, Wang L, He J, Li X, Hou N, Guo J, Niu C, Li C, Liu S, Xu J, Xie Y, Zhang D, Shen X, Lu L, Geng D, Chen P, Jiang L, Wang L, Li H, Malnoy M, Deng C, Zou Y, Li C, Zhan X, Dong Y, Notaguchi M, Ma F, Xu Q, Guan Q. Chromosome-scale reference genome provides insights into the genetic origin and grafting-mediated stress tolerance of Malus prunifolia. Plant Biotechnol J. 2022 Jun;20(6):1015-1017. doi: 10.1111/pbi.13817.
AbstractGrafting, an ancient horticultural cultivation technique, is essential for commercial apple (Malus × domestica Borkh.) production. M. prunifolia ‘Fupingqiuzi’ is used as a common apple rootstock due to its known tolerances to abiotic and biotic stresses. However, the genetic origin and evolutionary history of M. prunifolia are largely unknown, as are the molecular bases underlying its innate stress tolerance characteristics and ability to graft-transmit stress tolerance to the scion. Here, we present a high-quality chromosome-scale genome sequence of M. prunifolia ‘Fupingqiuzi’ (2n = 2x = 34) assembled using a combined strategy of Illumina short reads, PacBio long reads, and Hi-C data (Figure S1, Tables S1-S3). The total length of the assembly was 712 Mb, with a scaffold N50 of 41.6 Mb (Figure 1a). Approximately 98.6% of the contigs were anchored into 17 pseudochromosomes (Figure 1b). Over 91.36% of non-redundant and single-mapped mate-pair reads were concordant pairs, indicating that Hi-C anchoring has high accuracy. BUSCO revealed a completeness rate of 95.3% (Table S4). A total of 44 997 protein-coding genes were predicted, with an average gene length of 5516 bp. In addition, 1785 non-coding RNA genes and 484 Mb of repetitive sequences were detected in the ‘Fupingqiuzi’ genome (Figure 1a, Tables S5-S6).
The Malus prunifolia Fupingqiuzi Genome v1.0 Assembly file is available in FASTA format.
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| Chromosomes (FASTA file) | Malus_prunifolia_Fupingqiuzi.genome_sequence.fasta.gz |
The Malus prunifolia Fupingqiuzi Genome v1.0 genome gene prediction files are available in GFF3 and FASTA format.
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| Genes (GFF3 file) | Malus_prunifolia_Fupingqiuzi.gene_model.gff3.gz |
| CDS sequences (FASTA file) | Malus_prunifolia_Fupingqiuzi.CDS.fasta.gz |
| Protein sequences (FASTA file) | Malus_prunifolia_Fupingqiuzi.proteins.fasta.gz |
Functional annotation for the Malus prunifolia Fupingqiuzi Genome v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
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| Domain from InterProScan | Malus_prunifolia_Fupingqiuzi_Genome_v1.0.Pfam.tsv.gz |
Malus S genes Nucleotide
Malus S genes Protein