Pyrus Communis Bartlett DH Genome v2.0 proteins

Human-Readable NamePyrus Communis Bartlett DH Genome v2.0 proteins
Database NamePyrusCommunis_BartlettDHv2.0.pep.fasta
Database Typeprotein
FASTA Header Formatdefault
External DatabaseJBrowse for Pyrus Communis BartlettDH v2.0 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

Pyrus Communis Bartlett DH Genome v2.0 transcripts

Human-Readable NamePyrus Communis Bartlett DH Genome v2.0 transcripts
Database NamePyrusCommunis_BartlettDHv2.0.cds.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseGDR
RegEx/^(\S+).*/
Link-out Typelink

Pyrus Communis Bartlett DH Genome v2.0 chromosomes

Human-Readable NamePyrus Communis Bartlett DH Genome v2.0 chromosomes
Database NamePyrusCommunis_BartlettDHv2.0.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for Pyrus Communis BartlettDH v2.0 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

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[more]

Resource Titles: 
Assembly
Gene Predictions
Download
Homology
Functional Analysis
Transcript Alignments
Resource Blocks: 

Downloads

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

 

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

 

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 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 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 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

Fragaria_vesca_v4.0.a2 proteins

Human-Readable NameFragaria_vesca_v4.0.a2 proteins
Database NameFragaria_vesca_v4.0.a2_proteins.fa
Database Typeprotein
FASTA Header Formatdefault
External DatabaseJBrowse for Fragaria vesca v4.0.a1 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

Fragaria_vesca_v4.0.a2 transcripts

Human-Readable NameFragaria_vesca_v4.0.a2 transcripts
Database NameFragaria_vesca_v4.0.a2_transcripts.fa
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseGDR
RegEx/^(\S+).*/
Link-out Typelink

Reference

Yongping Li, Mengting Pi, Qi Gao, Zhongchi Liu & Chunying Kang.(2019). Updated annotation of the wild strawberry Fragaria vesca V4 genome. Horticulture Researchvolume 6, Article number: 61

Background

The cultivated strawberry (Fragaria × ananassa, 8x) is an economically important crop worldwide. The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry as well as the Rosaceae family. F. vesca... [more]

Resource Titles: 
Download
Gene Predictions
Homology
Functional Analysis
Resource Blocks: 

All 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 do download.  Alternatively, you can use the FTP repository for bulk download.

The Fragaria vesca v4.0.a2 gene prediction files are available in FASTA and GFF3 formats.

Downloads

Genes (GFF3 file) Fragaria_vesca_v4.0.a2.genes.gff3.gz
CDS (FASTA file) Fragaria_vesca_v4.0.a2.cds.fa.gz
Proteins (FASTA file) Fragaria_vesca_v4.0.a2.proteins.fa.gz

Homology of the Fragaria vesca genome v4.0.a2 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

Fragaria vesca v4.0.a2 proteins with NCBI nr homologs (EXCEL file) Fvesca_v4.0.a2_vs_nr.xlsx.gz
Fragaria vesca v4.0.a2 proteins with NCBI nr (FASTA file) Fvesca_v4.0.a2_vs_nr_hit.fasta.gz
Fragaria vesca v4.0.a2 proteins without NCBI nr (FASTA file) Fvesca_v4.0.a2_vs_nr_noHit.fasta.gz
Fragaria vesca v4.0.a2 proteins with arabidopsis (Araport11) homologs (EXCEL file) Fvesca_v4.0.a2_vs_arabidopsis.xlsx.gz
Fragaria vesca v4.0.a2 proteins with arabidopsis (Araport11) (FASTA file) Fvesca_v4.0.a2_vs_arabidopsis_hit.fasta.gz
Fragaria vesca v4.0.a2 proteins without arabidopsis (Araport11) (FASTA file) Fvesca_v4.0.a2_vs_arabidopsis_noHit.fasta.gz
Fragaria vesca v4.0.a2 proteins with SwissProt homologs (EXCEL file) Fvesca_v4.0.a2_vs_swissprot.xlsx.gz
Fragaria vesca v4.0.a2 proteins with SwissProt (FASTA file) Fvesca_v4.0.a2_vs_swissprot_hit.fasta.gz
Fragaria vesca v4.0.a2 proteins without SwissProt (FASTA file) Fvesca_v4.0.a2_vs_swissprot_noHit.fasta.gz
Fragaria vesca v4.0.a2 proteins with TrEMBL homologs (EXCEL file) Fvesca_v4.0.a2_vs_trembl.xlsx.gz
Fragaria vesca v4.0.a2 proteins with TrEMBL (FASTA file) Fvesca_v4.0.a2_vs_trembl_hit.fasta.gz
Fragaria vesca v4.0.a2 proteins without TrEMBL (FASTA file) Fvesca_v4.0.a2_vs_trembl_noHit.fasta.gz

 

Functional annotation for the Fragaria vesca genome v4.0.a2 are available for download below. The Fragaria vesca genome v4.0.a2 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 Fvesca_v4.0.a2_genes2GO.xlsx.gz
IPR assignments from InterProScan Fvesca_v4.0.a2_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Fvesca_v4.0.a2_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Fvesca_v4.0.a2_KEGG-pathways.xlsx.gz

 

  • Travisany D, lAyala-Raso A, Genova AD, Monsalve L, Bernales M, Martínez JP, González-Agüero M, Defilippi B, Cherian S, Maass A, Fuentesc L. RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus "Heritage") revealed several candidate genes involved in fruit development and ripening. Scientia Horticulturae 2019 August 25; 254:26-34.
Using Illumina HiSeq ™ 2000 sequencing platform (100 bp double-end reads), we performed transcriptome analysis of flower (F), green (G) and pink (P) fruit stages of red raspberry. Transcriptome was obtained by the de-novo assembly of 298 Million high-quality reads through Trinity assembler, out of the 41,650 high quality transcripts, 18,171 coding sequences were successfully characterized using databases such as UniProtKB, NCBI Non-Redundant, K... [more]
  • Yu C, Luo L, Pan H, Guo X, Wan H, Zhang Q. Filling gaps with construction of a genetic linkage map in tetraploid roses. Frontiers in plant science. 2015; 5:796.
Rose (Rosa sp.) is one of the most economically important ornamental crops worldwide. The present work contains a genetic linkage map for tetraploid roses that was constructed from an F1 segregation population using AFLPs and SSRs on 189 individuals. The preliminary ‘Yunzheng Xiawei’ and ‘Sun City’ maps consisted of 298 and 255 markers arranged into 26 and 32 linkage groups, respectively. The recombined parental maps covered 737 and 752 c... [more]
  • Howard N, van de Weg E, Bedford D, Peace C, Vanderzande S, Clark M, Teh S, Cai L, Luby J. Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus× domestica) pedigree-connected SNP data set. Horticulture Research. 2017; (4)17003.
The apple (Malus × domestica) cultivar Honeycrisp has become important economically and as a breeding parent. An earlier study with SSR markers indicated the original recorded pedigree of ‘Honeycrisp’ was incorrect and ‘Keepsake’ was identified as one putative parent, the other being unknown. The objective of this study was to verify ‘Keepsake’ as a parent and identify and genetically describe the unknown parent and its grandparen... [more]