Prunus Mandshurica CH264_4 Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus Mandshurica CH264_4 Whole Genome v1.0 Assembly & Annotation
MethodFalcon/Falcon-Unzip/SMARTdenovo/Ra (na)
SourceLong-reads(Oxford Nanopore Technologies or Pacific Biosciences)and Illumina
Date performed2021-03-09

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Homology

Homology of the Prunus mandshurica CH264_4 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 mandshurica CH264_4 v1.0 proteins with NCBI nr homologs (EXCEL file) Pmandshurica_CH264_4_v1.0_vs_nr.xlsx.gz
Prunus mandshurica CH264_4 v1.0 proteins with NCBI nr (FASTA file) Pmandshurica_CH264_4_v1.0_vs_nr_hit.fasta.gz
Prunus mandshurica CH264_4 v1.0 proteins without NCBI nr (FASTA file) Pmandshurica_CH264_4_v1.0_vs_nr_noHit.fasta.gz
Prunus mandshurica CH264_4 v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Pmandshurica_CH264_4_v1.0_vs_arabidopsis.xlsx.gz
Prunus mandshurica CH264_4 v1.0 proteins with arabidopsis (Araport11) (FASTA file) Pmandshurica_CH264_4_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus mandshurica CH264_4 v1.0 proteins without arabidopsis (Araport11) (FASTA file) Pmandshurica_CH264_4_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus mandshurica CH264_4 v1.0 proteins with SwissProt homologs (EXCEL file) Pmandshurica_CH264_4_v1.0_vs_swissprot.xlsx.gz
Prunus mandshurica CH264_4 v1.0 proteins with SwissProt (FASTA file) Pmandshurica_CH264_4_v1.0_vs_swissprot_hit.fasta.gz
Prunus mandshurica CH264_4 v1.0 proteins without SwissProt (FASTA file) Pmandshurica_CH264_4_v1.0_vs_swissprot_noHit.fasta.gz
Prunus mandshurica CH264_4 v1.0 proteins with TrEMBL homologs (EXCEL file) Pmandshurica_CH264_4_v1.0_vs_trembl.xlsx.gz
Prunus mandshurica CH264_4 v1.0 proteins with TrEMBL (FASTA file) Pmandshurica_CH264_4_v1.0_vs_trembl_hit.fasta.gz
Prunus mandshurica CH264_4 v1.0 proteins without TrEMBL (FASTA file) Pmandshurica_CH264_4_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

The Prunus mandshurica CH264_4 Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) pMandshurica_CH264_4_v1.0.fasta.gz

 

Gene Predictions

The Prunus mandshurica CH264_4 v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) pMandshurica_CH264_4_v1.0.proteins.fasta.gz
Genes (GFF3 file) pMandshurica_CH264_4_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus mandshurica CH264_4 Genome v1.0 are available for download below. The Prunus mandshurica CH264_4 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 Pmandshurica_CH264_4_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Pmandshurica_CH264_4_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Pmandshurica_CH264_4_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Pmandshurica_CH264_4_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 fragaria 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 mandshurica CH264_4 _v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus mandshurica CH264_4 _v1.0_m.x.domestica_GDR_reftransV1
fragaria avium GDR RefTrans v1 Prunus mandshurica CH264_4 _v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Prunus mandshurica CH264_4 _v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus mandshurica CH264_4 _v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus mandshurica CH264_4 _v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus mandshurica CH264_4 _v1.0_rubus_GDR_reftransV2