Malus prunifolia Fupingqiuzi Genome v1.0 Assembly & Annotation

Analysis NameMalus prunifolia Fupingqiuzi Genome v1.0 Assembly & Annotation
SourceMalus prunifolia Fupingqiuzi Genome v1.0, Illumina, PacBio and Hi-C
Date performed2022-04-14


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. A Chromosome-Scale Reference Genome Provides Insights into the Genetic Origin and Grafting-Mediated Stress Tolerance of Malus prunifolia.. Plant biotechnology journal. 2022 Mar 29  DOI: 10.1111/pbi.13817.


Malus prunifolia is a species of crabapple and  M. prunifolia ‘Fupingqiuzi’ is used as a common apple rootstock due to its known tolerances to abiotic and biotic stresses. This paper 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. The total length of the assembly was 712 Mb, with a scaffold N50 of 41.6 Mb. Approximately 98.6% of the contigs were anchored into 17 pseudochromosomes. 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% . 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.


The Malus prunifolia Fupingqiuzi Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) Malus_prunifolia_Fupingqiuzi v1.0.fasta.gz


Gene Predictions

The Malus prunifolia Fupingqiuzi v1.0 genome gene prediction files are available in FASTA and GFF3 formats.


Protein sequences  (FASTA file) Malus_prunifolia_Fupingqiuzi v1.0.proteins.fasta.gz
CDS  (FASTA file) Malus_prunifolia_Fupingqiuzi v1.0.cds.fasta.gz
Genes (GFF3 file) Malus_prunifolia_Fupingqiuzi v1.0.genes.gff3.gz