Prunus salicina Zhongli No. 6 Whole Genome v1.0 Assembly & Annotation
Huang Z, Shen F, Chen Y, Cao K, Wang L. Chromosome-scale Genome Assembly and Population Genomics Provide Insights into the Adaptation, Domestication, and Flavonoid Metabolism of Chinese Plum. Plant J. 2021 Sep 2. doi: 10.1111/tpj.15482.
Plum is one of the most important horticultural crops worldwide, possessing extensive genetic diversity and high economic value and providing us vitamins, minerals, fiber, and antioxidant compounds for healthy diets. At present, the most commercially produced plums are the Chinese plum (Prunus salicina L., 2n = 2× = 16) and European plum (Prunus domestica L., 2n = 6× = 48). China is currently the largest plum (and sloes) producer, with an annual production of 6,801,187 metric tons in 2018, accounting for 53.9% of the world’s total.
Genome facts and statistics
Chinese plum v1.0 was generated from DNA from a diploid Chinese cultivar 'Zhongli No. 6'. Chinese plum v1.0 currently consists of 8 pseudomolecules (scaffolds) representing the 8 chromosomes of plum. The genome sequencing consisted of approximately 117 fold whole genome shotgun sequencing employing Nanopore sequencing, and was assembled using CANU and SMARTdenvo. The assembled plum scaffolds cover nearly 99% of the genome. The high-quality genome assembly was comprised of 318.6 Mb (contig N50 length = 2.3 Mb) with 8 pseudomolecules. We identified 27481 high-confidence protein-coding genes. The annotated genes covered 95.9% of the complete BUSCO genes and ~92.28% of the annotated genes were expressed in at least one tissue or homologous to known proteins, which suggested that our genes annotation was very complete.
Contacts: Zhenyu Huang (firstname.lastname@example.org) & Fei Shen (email@example.com)
Homology of the Prunus salicina genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.
All assembly and annotation files are available for download by selecting the desired data type in the left-hand side bar. Each data type page will provide a description of the available files and links to download.
Functional annotation for the Prunus salicina genome v1.0 are available for download below. The Prunus salicina genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Prunus salicina genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.