| Analysis Name | Prunus armeniaca ASM2042406v1 Assembly & Annotation |
| Sequencing technology | Oxford Nanopore |
| Assembly method | Canu v. 1.0; smartdenovo v. 1.0 |
| Release Date | 2021-10-12 |
Zhang Q, Zhang D, Yu K, Ji J, Liu N, Zhang Y, Xu M, Zhang YJ, Ma X, Liu S, Sun WH, Yu X, Hu W, Lan SR, Liu ZJ, Liu W. Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm. Hortic Res. 2021 Oct 1;8(1):215. doi: 10.1038/s41438-021-00650-8.
AbstractThe genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement. However, little is known about the factors that shape and maintain genetic diversity. Here, we assembled a high-quality chromosome-level reference of the Chinese common apricot ‘Yinxiangbai’, and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries. We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries. We also detected seven migration events among different apricot groups, where 27% of the genome was identified as being introgressed. Remarkably, we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups. Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.
Assembly statistics
| Genome sizeh | 251.3 Mb |
| Total ungapped lengthh | 251.2 Mb |
| Number of chromosomesh | 8 |
| Number of scaffoldsh | 228 |
| Scaffold N50h | 31 Mb |
| Scaffold L50h | 4 |
| Number of contigsh | 507 |
| Contig N50h | 3.2 Mb |
| Contig L50h | 24 |
| GC percenth | 37.5 |
| Genome coverageh | 294.0x |
| Assembly levelh | Chromosome |
The Prunus armeniaca ASM2042406v1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_020424065.1_ASM2042406v1_genomic.fna.gz |
The Prunus armeniaca ASM2042406v1 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | Prunus_armeniaca_ASM2042406v1.gff.gz |
| CDS sequences (FASTA file) | GCA_020424065.1_ASM2042406v1_cds_from_genomic.fna.gz |
| Protein sequences (FASTA file) | GCA_020424065.1_ASM2042406v1_protein.faa.gz |
Functional annotation for the Prunus armeniaca ASM2042406v1 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).
Downloads
| Domain from InterProScan | Prunus_armeniaca_Yinxiangbai_Xing_ASM2042406v1.Pfam.tsv.gz |
Prunus S genes Nucleotide
Prunus S genes Protein