| Analysis Name | Prunus fruticosa JKI_Pf_1.0 Assembly & Annotation |
| Sequencing technology | Oxford Nanopore PromethION |
| Assembly method | miniasm v. 0.2-r137-dirty; racon v. 1.4.10; medaka v. 1.01; purge dups v. 1.0.1 |
| Release Date | 2021-06-03 |
Grimplet J. Genomic and Bioinformatic Resources for Perennial Fruit Species. Curr Genomics. 2022 Aug 11;23(4):217-233. doi: 10.2174/1389202923666220428102632.
AbstractIn the post-genomic era, data management and development of bioinformatic tools are critical for the adequate exploitation of genomics data. In this review, we address the actual situation for the subset of crops represented by the perennial fruit species. The agronomical singularity of these species compared to plant and crop model species provides significant challenges on the implementation of good practices generally not addressed in other species. Studies are usually performed over several years in non-controlled environments, usage of rootstock is common, and breeders heavily rely on vegetative propagation. A reference genome is now available for all the major species as well as many members of the economically important genera for breeding purposes. Development of pangenome for these species is beginning to gain momentum which will require a substantial effort in term of bioinformatic tool development. The available tools for genome annotation and functional analysis will also be presented.
Assembly statistics
| Genome size | 375.3 Mb |
| Total ungapped length | 375.2 Mb |
| Number of chromosomes | 8 |
| Number of scaffolds | 57 |
| Scaffold N50 | 43.8 Mb |
| Scaffold L50 | 4 |
| Number of contigs | 1,247 |
| Contig N50 | 530.9 kb |
| Contig L50 | 201 |
| GC percent | 38 |
| Genome coverage | 97.0x |
| Assembly level | Chromosome |
The Prunus fruticosa JKI_Pf_1.0 Assembly file is available in FASTA format.
Downloads
| Chromosomes (FASTA file) | GCA_018703695.1_JKI_Pf_1.0_genomic.fna.gz |
The Prunus fruticosa JKI_Pf_1.0 genome gene prediction files are not available.
Downloads
| Genes (GFF3 file) | - |
| CDS sequences (FASTA file) | - |
| Protein sequences (FASTA file) | - |
Functional annotation for the Prunus fruticosa JKI_Pf_1.0 is not available for download below.
Downloads
| Domain from InterProScan | - |
Prunus S genes Nucleotide
Prunus S genes Protein