Prunus salicina Sanyueli Whole Genome v2.0 Assembly & Annotation

Overview
Analysis NamePrunus salicina Sanyueli Whole Genome v2.0 Assembly & Annotation
MethodFALCON (v0.3.0)
SourcePacBio and Illumina reads
Date performed2020-10-10

Publication:
Chaoyang Liu, Chao Feng, Weizhuo Peng, Jingjing Hao, Juntao Wang, Jianjun Pan, Yehua He. Chromosome-level draft genome of a diploid plum (Prunus salicina). GigaScience, Volume 9, Issue 12, December 2020, giaa130, https://doi.org/10.1093/gigascience/giaa130

Data submitted by Chaoyang Liu, South China Agricultural University, Guangzhou, China

Overview: 
Plums are one of the most economically important Rosaceae fruit crops and are produced throughout the world. Prunus salicina is an important diploid (2x=2n=16) plum species that predominates in the modern commercial production of plums. However, the genomic information for P. salicina as well as most plum species is scarce. Here we present a chromosome-level genome assembly of P. salicina with the combination of PacBio sequencing, Illumina Sequencing and Hi-C technology. The assembly has a total size of 284.2 Mb, with contig N50 of 1.8Mb and scaffold N50 of 32.3Mb. 96.56% of the P. salicina assembled sequences were anchored onto 8 pseudochromosomes. De novo, homology-based, and RNA-seq methods were used together to predict were used together to predict 24,448 protein-coding genes, 97.90% of which were functionally annotated. BUSCO analysis showed 95.7% complete genes. CEGMA assessment showed that our assembly captured 234 (94.35%) of the 248 ultra-conserved core eukaryotic genes, of which 229 (92.34%) were complete. 

Homology

Homology of the Prunus salicina Sanyueli Genome v2.0 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 Sanyueli v2.0 proteins with NCBI nr homologs (EXCEL file) psalicina_v2.0_vs_nr.xlsx.gz
Prunus salicina Sanyueli v2.0 proteins with NCBI nr (FASTA file) psalicina_v2.0_vs_nr_hit.fasta.gz
Prunus salicina Sanyueli v2.0 proteins without NCBI nr (FASTA file) psalicina_v2.0_vs_nr_noHit.fasta.gz
Prunus salicina Sanyueli v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) psalicina_v2.0_vs_arabidopsis.xlsx.gz
Prunus salicina Sanyueli v2.0 proteins with arabidopsis (Araport11) (FASTA file) psalicina_v2.0_vs_arabidopsis_hit.fasta.gz
Prunus salicina Sanyueli v2.0 proteins without arabidopsis (Araport11) (FASTA file) psalicina_v2.0_vs_arabidopsis_noHit.fasta.gz
Prunus salicina Sanyueli v2.0 proteins with SwissProt homologs (EXCEL file) psalicina_v2.0_vs_swissprot.xlsx.gz
Prunus salicina Sanyueli v2.0 proteins with SwissProt (FASTA file) psalicina_v2.0_vs_swissprot_hit.fasta.gz
Prunus salicina Sanyueli v2.0 proteins without SwissProt (FASTA file) psalicina_v2.0_vs_swissprot_noHit.fasta.gz
Prunus salicina Sanyueli v2.0 proteins with TrEMBL homologs (EXCEL file) psalicina_v2.0_vs_trembl.xlsx.gz
Prunus salicina Sanyueli v2.0 proteins with TrEMBL (FASTA file) psalicina_v2.0_vs_trembl_hit.fasta.gz
Prunus salicina Sanyueli v2.0 proteins without TrEMBL (FASTA file) psalicina_v2.0_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 GDR data repository.

Assembly

The Prunus salicina Sanyueli Genome v2.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) psalicina_v2.0.fasta.gz
Repeats (GFF3 file) psalicina_v2.0.repeats.gff3.gz

 

Gene Predictions

The Prunus salicina Sanyueli v2.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) psalicina_v2.0.proteins.fasta.gz
Tanscript sequences (FASTA file) psalicina_v2.0.transcripts.fasta.gz
Genes (GFF3 file) psalicina_v2.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus salicina Sanyueli Genome v2.0 are available for download below. The Prunus salicina Genome v2.0 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_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan psalicina_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways psalicina_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs psalicina_v2.0_KEGG-pathways.xlsx.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 Sanyueli_v2.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus salicina Sanyueli_v2.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus salicina Sanyueli_v2.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus salicina Sanyueli_v2.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus salicina Sanyueli_v2.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus salicina Sanyueli_v2.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus salicina Sanyueli_v2.0_rubus_GDR_reftransV2