Pyrus communis Bartlett DH Genome v2.0

Overview
Analysis NamePyrus communis Bartlett DH Genome v2.0
MethodPacBio, Illumina, Bionano and Hi-C (Canu assembly)
SourceBartlett pear DH genome v2
Date performed2019-05-28

Publication

Gareth Linsmith, Stephane Rombauts, Sara Montanari, Cecilia H. Deng, Jean-Marc Celton, Philippe Guérif, Chang Liu, Rolf Lohaus, Jason D. Zurn, Alessandro Cestaro, Nahla V. Bassil, Linda V. Bakker, Elio Schijlen, Susan E. Gardiner, Yves Lespinasse, Charles-Eric Durel, Riccardo Velasco, David Neale, David Chagné, Yves Van de Peer, Michela Troggio, Luca Bianco. Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.). doi: https://doi.org/10.1101/651778

Abstract

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

Assembly

Downloads

Chromosome(FASTA file) Pyrus communis BartlettDH v2.0.fasta.gz

 

Gene Predictions

The Pyrus communis Bartlett DH v2.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Transcript CDS sequences (FASTA file) Pyrus communis Bartlett DH v2.transcripts.fasta.gz
Protein sequences  (FASTA file) Pyrus communis Bartlett DH v2.proteins.fasta.gz
Genes (GFF3 file) Pyrus communis Bartlett DH.genes.v2.gff3.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.

Homology

Homology of the Pyrus communis BartlettDH 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

Pyrus communis DH v2.0 proteins with NCBI nr homologs (EXCEL file) PCommunis_DH_v2.0_vs_nr.xlsx.gz
Pyrus communis DH v2.0 proteins with NCBI nr (FASTA file) PCommunis_DH_v2.0_vs_nr_hit.fasta.gz
Pyrus communis DH v2.0 proteins without NCBI nr (FASTA file) PCommunis_DH_v2.0_vs_nr_noHit.fasta.gz
Pyrus communis DH v2.0 proteins with arabidopsis homologs (EXCEL file) PCommunis_DH_v2.0_vs_arabidopsis.xlsx.gz
Pyrus communis DH v2.0 proteins with arabidopsis (FASTA file) PCommunis_DH_v2.0_vs_arabidopsis_hit.fasta.gz
Pyrus communis DH v2.0 proteins without arabidopsis (FASTA file) PCommunis_DH_v2.0_vs_arabidopsis_noHit.fasta.gz
Pyrus communis DH v2.0 proteins with SwissProt homologs (EXCEL file) PCommunis_DH_v2.0_vs_swissprot.xlsx.gz
Pyrus communis DH v2.0 proteins with SwissProt (FASTA file) PCommunis_DH_v2.0_vs_swissprot_hit.fasta.gz
Pyrus communis DH v2.0 proteins without SwissProt (FASTA file) PCommunis_DH_v2.0_vs_swissprot_noHit.fasta.gz
Pyrus communis DH v2.0 proteins with TrEMBL homologs (EXCEL file) PCommunis_DH_v2.0_vs_trembl.xlsx.gz
Pyrus communis DH v2.0 proteins with TrEMBL (FASTA file) PCommunis_DH_v2.0_vs_trembl_hit.fasta.gz
Pyrus communis DH v2.0 proteins without TrEMBL (FASTA file) PCommunis_DH_v2.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation files for the Pyrus communis Bartlett DH genome v2.0 are available for download below. The Pyrus communis DH 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 PCommunis_DH_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan PCommunis_DH_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs PCommunis_DH_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways PCommunis_DH_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 Pyrus communis 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 communis_BDH_v2.0_f.x.ananassa_GDR_reftransV1
Pyrus communis GDR RefTrans v1 Pyrus communis_BDH_v2.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Pyrus communis_BDH_v2.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Pyrus communis_BDH_v2.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pyrus communis_BDH_v2.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pyrus communis_BDH_v2.0_rubus_GDR_reftransV2