| Analysis Name | Prunus salicina Sanyueli_v2.0 Assembly & Annotation |
| Sequencing technology | PacBio and Illumina reads |
| Assembly method | FALCON (v0.3.0) |
| Release Date | 2020-10-10 |
Liu C, Feng C, Peng W, Hao J, Wang J, Pan J, He Y. Chromosome-level draft genome of a diploid plum (Prunus salicina). Gigascience. 2020 Dec 10;9(12):giaa130. doi: 10.1093/gigascience/giaa130.
AbstractBackground: Plums are one of the most economically important Rosaceae fruit crops and comprise dozens of species distributed across the world. Until now, only limited genomic information has been available for the genetic studies and breeding programs of plums. Prunus salicina, an important diploid plum species, plays a predominant role in modern commercial plum production. Here we selected P. salicina for whole-genome sequencing and present a chromosome-level genome assembly through the combination of Pacific Biosciences sequencing, Illumina sequencing, and Hi-C technology. Findings: The assembly had a total size of 284.2 Mb, with contig N50 of 1.78 Mb and scaffold N50 of 32.32 Mb. A total of 96.56% of the assembled sequences were anchored onto 8 pseudochromosomes, and 24,448 protein-coding genes were identified. Phylogenetic analysis showed that P. salicina had a close relationship with Prunus mume and Prunus armeniaca, with P. salicina diverging from their common ancestor ∼9.05 million years ago. During P. salicina evolution 146 gene families were expanded, and some cell wall–related GO terms were significantly enriched. It was noteworthy that members of the DUF579 family, a new class involved in xylan biosynthesis, were significantly expanded in P. salicina, which provided new insight into the xylan metabolism in plums. Conclusions: We constructed the first high-quality chromosome-level plum genome using Pacific Biosciences, Illumina, and Hi-C technologies. This work provides a valuable resource for facilitating plum breeding programs and studying the genetic diversity mechanisms of plums and Prunus species.
Assembly statistics
| Scaffolds total length (bp) | 284,209,110 |
| Scaffolds No. | 75 |
| Scaffolds N50 (bp) | 32,324,625 |
| Contigs total length (bp) | 284,189,410 |
| Contigs No. | 272 |
| Contigs N50 (bp) | 1,777,944 |
The Prunus salicina Sanyueli_v2.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | psalicina_v2.0.fasta.gz |
The Prunus salicina Sanyueli_v2.0 genome gene prediction files are available in GFF3 and FASTA format.
Downloads
| Genes (GFF3 file) | psalicina_v2.0.genes.gff3.gz |
| CDS sequences (FASTA file) | psalicina_v2.0.transcripts.fasta.gz |
| Protein sequences (FASTA file) | psalicina_v2.0.protein.fasta.gz |
Summary
| Query | Chr | Size(bp) | Coordinates | Domain |
| PsaSLF7.4 | Chr6 | 36292479 | 32829807-32830955 | F-box |
| PsaSLF7.2 | Chr6 | 36292479 | 32836287-32837765 | F-box |
| PsaSLF7.1 | Chr6 | 36292479 | 33268448-33269941 | F-box; F_box_assoc |
| PsaSLF7.3 | Chr6 | 36292479 | 33274938-33276416 | F-box |
| PsaSLF4 | Chr6 | 36292479 | 33699243-33697873 | F-box; F_box_assoc |
| PsaSLF2 | Chr6 | 36292479 | 33784750-33786024 | F-box; F_box_assoc |
| PsaSLF1 | Chr6 | 36292479 | 33822191-33820980 | F-box; F_box_assoc |
| PsaSFB | Chr6 | 36292479 | 33824425-33825555 | F-box; F_box_assoc |
| PsaSLF3 | Chr6 | 36292479 | 33856713-33857936 | F-box; F_box_assoc |
| PsaSLF5 | Chr6 | 36292479 | 33900514-33899336 | F-box; F_box_assoc |
| S-RNase | Chr6 | 36292479 | 33830243-33830168,33829876-33829692,33826993-33826583 | RNase_T2 |
Prunus salicina Sanyueli_v2.0 S genes Nucleotide
Prunus salicina Sanyueli_v2.0 S genes Protein