Prunus salicina Zhongli No. 6 Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus salicina Zhongli No. 6 Whole Genome v1.0 Assembly & Annotation
MethodCANU &SMATRdenovo (na)
SourcePrunus salicina Nanopore Reads
Date performed2020-08-16

Background

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.
The genome sequencing and assembly was conducted by Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science. 

Contacts: Zhenyu Huang (huangzhenyu@caas.cn) & Fei Shen (flynn123@cau.edu.cn)  

Publication

Manuscript in preparation

Homology Analysis

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. 

 

Protein Homologs

Prunus salicina v1.0 proteins with NCBI nr homologs (EXCEL file) psalicina_v1.0_vs_nr.xlsx.gz
Prunus salicina v1.0 proteins with NCBI nr (FASTA file) psalicina_v1.0_vs_nr_hit.fasta.gz
Prunus salicina v1.0 proteins without NCBI nr (FASTA file) psalicina_v1.0_vs_nr_noHit.fasta.gz
Prunus salicina v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) psalicina_v1.0_vs_arabidopsis.xlsx.gz
Prunus salicina v1.0 proteins with arabidopsis (Araport11) (FASTA file) psalicina_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus salicina v1.0 proteins without arabidopsis (Araport11) (FASTA file) psalicina_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus salicina v1.0 proteins with SwissProt homologs (EXCEL file) psalicina_v1.0_vs_swissprot.xlsx.gz
Prunus salicina v1.0 proteins with SwissProt (FASTA file) psalicina_v1.0_vs_swissprot_hit.fasta.gz
Prunus salicina v1.0 proteins without SwissProt (FASTA file) psalicina_v1.0_vs_swissprot_noHit.fasta.gz
Prunus salicina v1.0 proteins with TrEMBL homologs (EXCEL file) psalicina_v1.0_vs_trembl.xlsx.gz
Prunus salicina v1.0 proteins with TrEMBL (FASTA file) psalicina_v1.0_vs_trembl_hit.fasta.gz
Prunus salicina v1.0 proteins without TrEMBL (FASTA file) psalicina_v1.0_vs_trembl_noHit.fasta.gz

 

Download

All assembly and annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links to download.  Alternatively, you can browse all available files on the FTP repository.

Assembly

The Prunus salicina Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) psalicina_v1.0.fasta.gz

 

Gene Predictions

The Prunus salicina v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) psalicina_v1.0.proteins.fasta.gz
Tanscript sequences (FASTA file) psalicina_v1.0.transcripts.fasta.gz
Genes (GFF3 file) psalicina_v1.0.genes.gff3.gz

 

Functional Analysis

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).

Downloads

GO assignments from InterProScan psalicina_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan psalicina_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways psalicina_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs psalicina_v1.0_KEGG-pathways.xlsx.gz

 

Repeats

Downloads

Repeats (GFF3 file) psalicina_v1.0.repeats.gff3.gz
Transcript Alignments
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.

 

Fragaria x ananassa GDR RefTrans v1 Prunus salicina_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus salicina_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus salicina_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus salicina_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus salicina_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus salicina_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus salicina_v1.0_rubus_GDR_reftransV2