Prunus davidiana ZXST Haplotype Genome v1.0 Assembly & Annotation

Analysis NamePrunus davidiana ZXST Haplotype Genome v1.0 Assembly & Annotation
MethodALLPATHS-LG, Hifiasm (v0.16.1-r375)
SourcePrunus davidiana Illumina, PacBio Hifi and Hi-C Reads
Date performed2023-10-04


Wang J, Li Y, Wang X, Cao K, Chen C, Wu J, Fang W, Zhu G, Wang J, Zhao Y, Fan J, Liu S, Chen X, Li W, Bie H, Guo D, Xu Q, Wang L. Haplotype-resolved genome analyses of a heterozygous wild peach reveal the PdaWRKY4 conferring aphid resistance. Submitted to Nature Genetics.


Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, shows high resistance against aphids. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2699 Pda_hap1 specific and 2702 Pda_hap2 specific genes, and 1118 allele specific expressed genes. Genome composition indicated 4.1% of P. davidiana genome was non-peach origin, of which 94.5% is derived from almond. PdaWRKY4 is identified to confer aphid resistance, with a 9-bp deletion in its promoter of the resistant phenotype, which directly promotes synthesis of the anti-aphid metabolite betulin. We employ a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. This study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

Materials and Methods

In this study, “Zhouxingshantao 1” (ZXST, Prunus davidiana) from the National Germplasm Resource Repository of Peach at the Zhengzhou Fruit Research Institute, CAAS, China, was used to construct haplotype genomes. By sequencing the ZXST, a total of 29 Gb HiFi long reads, 24 Gb ONT long reads, and 40 Gb Hi-C reads were obtained. The k-mer distribution exhibited remarkable double peaks, indicating a highly heterozygous ZXST genome, with a heterozygosity rate of 1.12%. The genome was initially phased and assembled using HiFi and Hi-C reads, and gaps were further filled by ONT reads. Finally, a 501.7 Mb chromosome-level haplotype genome of ZXST with 16 pseudochromosomes was obtained, which could be divided into two haplotypes with sizes of 257.1 and 244.6 Mb, respectively. A total of 22,479 and 21,784 protein-coding genes were predicted in the Pda_hap1 and Pda_hap2 genomes, respectively, based on an integrative pipeline of de novo prediction, homology-based search, and RNA-seq evidence.


The Prunus davidiana ZXST Haplotype genome v1.0 assembly files are available in GFF3 and FASTA format.


Chromosomes (masked HAP 1) (FASTA file) Pdavidiana_Hap1.masked_V1.0.a1.fasta.gz
Chromosomes (masked HAP 2) (FASTA file) Pdavidiana_Hap2.masked_V1.0.a1.fasta.gz
Chromosomes (HAP 1) (FASTA file) Pdavidiana_Hap1_V1.0.a1.fasta.gz
Chromosomes (HAP 2) (FASTA file) Pdavidiana_Hap2_V1.0.a1.fasta.gz
Repeats (HAP 1) (GFF3 file) Pdavidiana_Hap1.repeats.gff.gz
Repeats (HAP 2) (GFF3 file) Pdavidiana_Hap2.repeats.gff.gz
Gene Predictions

The Prunus davidiana ZXST Haplotype genome v1.0 gene prediction files are available in GFF3 and FASTA format.


Genes (HAP 1) (GFF3 file) Pdavidiana_Hap1_V1.0.a1.genes.gff3.gz
Genes (HAP 2) (GFF3 file) Pdavidiana_Hap2_V1.0.a1.genes.gff3.gz
Protein sequences (HAP 1) (FASTA file) Pdavidiana_Hap1_V1.0.a1.pep.fasta.gz
Protein sequences (HAP 2) (FASTA file) Pdavidiana_Hap2_V1.0.a1.pep.fasta.gz
CDS sequences (HAP 1) (FASTA file) Pdavidiana_Hap1_V1.0.a1.cds.fasta.gz
CDS sequences (HAP 2) (FASTA file) Pdavidiana_Hap2_V1.0.a1.cds.fasta.gz