Prunus mira Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus mira Whole Genome v1.0 Assembly & Annotation
MethodFALCON, ALLPATHS-LG
SourcePrunus mira Illumina and PacBio Reads
Date performed2020-07-14

Publication
Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation (to be submitted by Cao Ke at Zhengzhou fruit research institute, CAAS, China)


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. mira is an attractive model for studying high-altitude adaptability of perennial plants because it originated in the Qinghai-Tibet plateau in China.

Genome facts and statistics
The high-quality genome of P. mira was assembled using a more than 100-years old tree through a combination of PacBio, Illumina, and Hi-C (High-throughput chromosome conformation capture) platforms. After estimating the genome size using the k-mer method, a total of 597.0× coverage of sequences were generated and used for genome assembly. 
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 13.93 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 657 scaffolds were anchored and 93.4% of them were allocated to eight pseudochromosomes. The contig N50 and scaffold N50 sizes of the final assembly were 443.7 kb and 27.44 Mb, respectively.
Gene prediction was performed using a combination of homology, ab initio and transcriptome based approaches resulting in 28,943 protein-coding genes in P. mira.

Homology Analysis

Homology of the Prunus mira 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 mira v1.0 proteins with NCBI nr homologs (EXCEL file) pmira_v1.0_vs_nr.xlsx.gz
Prunus mira v1.0 proteins with NCBI nr (FASTA file) pmira_v1.0_vs_nr_hit.fasta.gz
Prunus mira v1.0 proteins without NCBI nr (FASTA file) pmira_v1.0_vs_nr_noHit.fasta.gz
Prunus mira v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pmira_v1.0_vs_arabidopsis.xlsx.gz
Prunus mira v1.0 proteins with arabidopsis (Araport11) (FASTA file) pmira_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus mira v1.0 proteins without arabidopsis (Araport11) (FASTA file) pmira_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus mira v1.0 proteins with SwissProt homologs (EXCEL file) pmira_v1.0_vs_swissprot.xlsx.gz
Prunus mira v1.0 proteins with SwissProt (FASTA file) pmira_v1.0_vs_swissprot_hit.fasta.gz
Prunus mira v1.0 proteins without SwissProt (FASTA file) pmira_v1.0_vs_swissprot_noHit.fasta.gz
Prunus mira v1.0 proteins with TrEMBL homologs (EXCEL file) pmira_v1.0_vs_trembl.xlsx.gz
Prunus mira v1.0 proteins with TrEMBL (FASTA file) pmira_v1.0_vs_trembl_hit.fasta.gz
Prunus mira v1.0 proteins without TrEMBL (FASTA file) pmira_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 mira Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) pmira_v1.0.fasta.gz

 

Gene Predictions

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

Downloads

Protein sequences  (FASTA file) pmira_v1.0.proteins.fasta.gz
Genes (GFF3 file) pmira_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus mira genome v1.0 are available for download below. The Prunus mira 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 pmira_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pmira_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pmira_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pmira_v1.0_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 mira 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 mira_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus mira_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus mira_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus mira_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus mira_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus mira_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus mira_v1.0_rubus_GDR_reftransV2