| Analysis Name | Prunus tenella XJ1 Assembly & Annotation |
| Sequencing technology | PacBio |
| Assembly method | AllPaths |
| Release Date | 2023-04-19 |
Qin Y, Zhao H, Han H, Zhu G, Wang Z, Li F. Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella. Int J Mol Sci. 2023 Jul 21;24(14):11735. doi: 10.3390/ijms241411735.
AbstractPrunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources.
Assembly statistics
| Genome size (bp) | 231,208,648 |
| GC content | 38.81% |
| Chromosomes sequence No. | 8 |
| Genome sequence No. | 479 |
| Maximum genome sequence length (bp) | 44,825,466 |
| Minimum genome sequence length (bp) | 15,256 |
| Average genome sequence length (bp) | 482,690 |
| Genome sequence N50 (bp) | 25,637,364 |
| Genome sequence N90 (bp) | 1,233,122 |
| Assembly level | Chromosome |
The Prunus tenella XJ1 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GWHCBGA00000000.genome.fasta.gz |
The Prunus tenella XJ1 genome gene prediction files are not available.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | - |
| Protein sequences (FASTA file) | - |
Functional annotation for the Prunus tenella XJ1 is not available.
Downloads
| Domain from InterProScan | - |
Prunus S genes Nucleotide
Prunus S genes Protein