| Analysis Name | Prunus hongpingensis Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | hifiasm 0.19.6-r595 |
| Release Date | 2023-11-27 |
Dai X, Xiang S, Zhang Y, Yang S, Hu Q, Wu Z, Zhou T, Xiang J, Chen G, Tan X, Wang J, Ding J. Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis. Hortic Res. 2023 Oct 27;11(4):uhad215. doi: 10.1093/hr/uhad215.
AbstractApricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.
Assembly statistics
| Genome size (bp) | 275,107,020 |
| GC content | 38.56% |
| Chromosomes sequence No. | 8 |
| Genome sequence No. | 433 |
| Maximum genome sequence length (bp) | 45,286,100 |
| Minimum genome sequence length (bp) | 1,000 |
| Average genome sequence length (bp) | 635,351 |
| Genome sequence N50 (bp) | 26,886,200 |
| Genome sequence N90 (bp) | 274,000 |
| Assembly levelh | Chromosome |
The Prunus hongpingensis Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHDUBN00000000.genome.fasta.gz |
The Prunus hongpingensis genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | GWHDUBN00000000.gff.gz |
| CDS sequences (FASTA file) | GWHDUBN00000000.RNA.fasta.gz |
| Protein sequences (FASTA file) | GWHDUBN00000000.Protein.faa.gz |
Functional annotation for the Prunus hongpingensis is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Prunus_hongpingensis.Pfam.tsv.gz |
Prunus S genes Nucleotide
Prunus S genes Protein