Prunus davidiana Whole Genome v2.0 Assembly & Annotation

Overview
Analysis NamePrunus davidiana Whole Genome v2.0 Assembly & Annotation
MethodALLPATHS-LG
SourcePrunus davidiana Illumina, PacBio and Hi-C Reads
Date performed2021-09-15

Publication

The study has not been published yet. The initial title is named as below: Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation. And the manuscript has been submitted to bioRxiv.

Background

Peach (Prunus persica) is the third most produced fruit crop, and is widely cultivated in temperate and subtropical regions. Due to its small genome size, peach has been used as a model plant for comparative and functional genomic researches of the Rosaceae family. In 2013, a high-quality reference genome sequence of peach constructed with the Sanger whole-genome shotgun approach was released by International Peach Genome Initiative. It is well known that wild germplasm contributes a significant proportion of the genetic resources of major crop species, and significant phenotypic differences in fruit size, flavor, and stress tolerance were found among P. persica and its wild relatives, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. It is necessary to study genetic variations of peach and its wild relatives from a broader perspective, such as pan-genome analyses. P. dvaidiana is an attractive model for studying resistance mechanism for aphid, drought, and low temperature.

Genome facts and statistics

The genome of P. davidiana was assembled using variety “Zhouxing Shan Tao” through Illumina platforms. Illumina reads from the wild species of P. persica were assembled using ALLPATHS-LG, and gaps in the assemblies were filled using GapCloser V1.12. Mate-paired reads were then used to generate scaffolds using SSPACE. Illumina reads from the wild specie were assembled using ALLPATHS-LG, and gaps in the assemblies were filled using GapCloser V1.12. Mate-paired reads were then used to generate scaffolds using SSPACE. In additon, PacBio SMRT reads were de novo assembled using FALCON. Approximately 31.13 Gb of PacBio SMRT reads were first pairwise compared, and the longest 60 coverage of subreads were selected as seeds to do error correction. All PacBio SMRT reads were mapped back to the assembled contigs with Blast and the Arrow program implemented in SMRT Link (PacBio) was used for error correction with default parameters. The Illumina paired-end reads were then mapped to the corrected contigs to perform the second round of error correction. To further improve the continuity of the assembly, SSPACE (v3.0) was used to build scaffolds using reads from all the mate pair libraries. FragScaff v1-1 was further applied to build superscaffolds using the barcoded sequencing reads. Finally, Hi-C data were used to correct superscaffolds and cluster the scaffolds into pseudochromosomes. A total of 89.46% of them were allocated to eight pseudochromosomes. The contig N50 and scaffold N50 sizes of the final assembly were 22.64 Mb and 28.55 Mb, respectively. Gene prediction was performed using a combination of homology, ab initio and transcriptome based approaches resulting in 27,236 protein-coding genes in P. davidiana.

Homology Analysis

Homology of the Prunus davidiana 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 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Prunus davidiana v2.0 proteins with NCBI nr homologs (EXCEL file) pdavidiana_v2.0_vs_nr.xlsx.gz
Prunus davidiana v2.0 proteins with NCBI nr (FASTA file) pdavidiana_v2.0_vs_nr_hit.fasta.gz
Prunus davidiana v2.0 proteins without NCBI nr (FASTA file) pdavidiana_v2.0_vs_nr_noHit.fasta.gz
Prunus davidiana v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pdavidiana_v2.0_vs_arabidopsis.xlsx.gz
Prunus davidiana v2.0 proteins with arabidopsis (Araport11) (FASTA file) pdavidiana_v2.0_vs_arabidopsis_hit.fasta.gz
Prunus davidiana v2.0 proteins without arabidopsis (Araport11) (FASTA file) pdavidiana_v2.0_vs_arabidopsis_noHit.fasta.gz
Prunus davidiana v2.0 proteins with SwissProt homologs (EXCEL file) pdavidiana_v2.0_vs_swissprot.xlsx.gz
Prunus davidiana v2.0 proteins with SwissProt (FASTA file) pdavidiana_v2.0_vs_swissprot_hit.fasta.gz
Prunus davidiana v2.0 proteins without SwissProt (FASTA file) pdavidiana_v2.0_vs_swissprot_noHit.fasta.gz
Prunus davidiana v2.0 proteins with TrEMBL homologs (EXCEL file) pdavidiana_v2.0_vs_trembl.xlsx.gz
Prunus davidiana v2.0 proteins with TrEMBL (FASTA file) pdavidiana_v2.0_vs_trembl_hit.fasta.gz
Prunus davidiana v2.0 proteins without TrEMBL (FASTA file) pdavidiana_v2.0_vs_trembl_noHit.fasta.gz

 

Assembly

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

Downloads

Chromosomes (FASTA file) pdavidiana_v2.0.fasta.gz

 

Gene Predictions

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

Downloads

Protein sequences  (FASTA file) pdavidiana_v2.0.proteins.fasta.gz
Genes (GFF3 file) pdavidiana_v2.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus davidiana Genome v2.0 are available for download below. The Prunus davidiana 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 pdavidiana_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pdavidiana_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pdavidiana_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pdavidiana_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 davidiana 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 davidiana_v2.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus davidiana_v2.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus davidiana_v2.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus davidiana_v2.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus davidiana_v2.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus davidiana_v2.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus davidiana_v2.0_rubus_GDR_reftransV2