Pyrus pyrifolia Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NamePyrus pyrifolia Whole Genome v1.0 Assembly & Annotation
MethodFALCON (v1.8.1)
SourcePyrus Pyrifolia Whole Genome v1.0
Date performed2021-01-11

Publication

Shirasawa K, Itai A, Isobe S. Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki'.. DNA research : an international journal for rapid publication of reports on genes and genomes. 2021 Feb 26:dsab001. doi: 10.1093/dnares/dsab001.

Overview:

Aim The Japanese pear (P. pyrifolia) variety ‘Nijisseiki’ is valued for its superior flesh texture, which has led to its use as a breeding parent for most Japanese pear cultivars. However, in the absence of genomic resources for Japanese pear, the parents of the ‘Nijisseiki’ cultivar remain unknown, as does the genetic basis of its favorable texture. The genomes of pear and related species are complex due to ancestral whole genome duplication and high heterozygosity, and long-sequencing technology was used to address this

Methods and Results De novo assembly of PacBio Sequel long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6 Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. 

Conclusion and Perspective This is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

External site

Plant GARDEN 

Homology

Homology of the Pyrus pyrifolia 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

Pyrus pyrifolia v1.0 proteins with NCBI nr homologs (EXCEL file) Pyrus_pyrifolia_v1.0_vs_nr.xlsx.gz
Pyrus pyrifolia v1.0 proteins with NCBI nr (FASTA file) Pyrus_pyrifolia_v1.0_vs_nr_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without NCBI nr (FASTA file) Pyrus_pyrifolia_v1.0_vs_nr_noHit.fasta.gz
Pyrus pyrifolia v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Pyrus_pyrifolia_v1.0_vs_arabidopsis.xlsx.gz
Pyrus pyrifolia v1.0 proteins with arabidopsis (Araport11) (FASTA file) Pyrus_pyrifolia_v1.0_vs_arabidopsis_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without arabidopsis (Araport11) (FASTA file) Pyrus_pyrifolia_v1.0_vs_arabidopsis_noHit.fasta.gz
Pyrus pyrifolia v1.0 proteins with SwissProt homologs (EXCEL file) Pyrus_pyrifolia_v1.0_vs_swissprot.xlsx.gz
Pyrus pyrifolia v1.0 proteins with SwissProt (FASTA file) Pyrus_pyrifolia_v1.0_vs_swissprot_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without SwissProt (FASTA file) Pyrus_pyrifolia_v1.0_vs_swissprot_noHit.fasta.gz
Pyrus pyrifolia v1.0 proteins with TrEMBL homologs (EXCEL file) Pyrus_pyrifolia_v1.0_vs_trembl.xlsx.gz
Pyrus pyrifolia v1.0 proteins with TrEMBL (FASTA file) Pyrus_pyrifolia_v1.0_vs_trembl_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without TrEMBL (FASTA file) Pyrus_pyrifolia_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 side bar.  Each data type page will provide a description of the available files and links to download.

Assembly

The Pyrus pyrifolia Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Pyrus_pyrifolia_v1.0.fasta.gz

 

Gene Predictions

The Pyrus pyrifolia v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Transcript sequences  (FASTA file) Pyrus_pyrifolia_v1.0.transcripts.fasta.gz
CDS  (FASTA file) Pyrus_pyrifolia_v1.0.cds.fasta.gz
Protein sequences  (FASTA file) Pyrus_pyrifolia_v1.0.proteins.fasta.gz
Genes (GFF3 file) Pyrus_pyrifolia_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Pyrus pyrifolia Genome v1.0 are available for download below. The Pyrus pyrifolia 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 Pyrus_pyrifolia_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Pyrus_pyrifolia_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Pyrus_pyrifolia_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Pyrus_pyrifolia_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 Pyrus pyrifolia 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 Pyrus pyrifolia _v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Pyrus pyrifolia _v1.0_m.x.domestica_GDR_reftransV1
fragaria avium GDR RefTrans v1 Pyrus pyrifolia _v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Pyrus pyrifolia _v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Pyrus pyrifolia _v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pyrus pyrifolia _v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pyrus pyrifolia _v1.0_rubus_GDR_reftransV2