Prunus avium Tieton Genome v1.0 Assembly & Annotation

Publication:

Wang J, Liu W, Zhu D, Zhou X, Hong P, Zhao H, Tan Y, Chen X, Zong X, Xu L, Zhang L, Wei H, Liu Q. A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology. PeerJ. 2020 Jun 5;8:e9114. doi: 10.7717/peerj.9114. 

Overview:

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to ... [more]

Resources
Resource Links: 
View Assembly in JBrowse|https://www.rosaceae.org/jbrowse/index.html?data=data/prunus/paviumTieton_v1.0.a1&loc=
BLAST|/blast
View Synteny|/synview/search
Resource Titles: 
Assembly
Gene Predictions
Homology
Functional Analysis
Transcript Alignments
Download
Resource Blocks: 

The Prunus avium Tieton Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) paviumTieton_chromosome_v1.0.fasta.gz
Scaffolds (FASTA file) paviumTieton_scaffold_v1.0.fasta.gz

 

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

Downloads

Protein sequences  (FASTA file) paviumTieton_v1.0.proteins.fasta.gz
Genes (GFF3 file) paviumTieton_v1.0.genes.gff3.gz

 

Homology of the Prunus avium Tieton 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 avium Tieton v1.0 proteins with NCBI nr homologs (EXCEL file) paviumTieton_v1.0_vs_nr.xlsx.gz
Prunus avium Tieton v1.0 proteins with NCBI nr (FASTA file) paviumTieton_v1.0_vs_nr_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without NCBI nr (FASTA file) paviumTieton_v1.0_vs_nr_noHit.fasta.gz
Prunus avium Tieton v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) paviumTieton_v1.0_vs_arabidopsis.xlsx.gz
Prunus avium Tieton v1.0 proteins with arabidopsis (Araport11) (FASTA file) paviumTieton_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without arabidopsis (Araport11) (FASTA file) paviumTieton_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus avium Tieton v1.0 proteins with SwissProt homologs (EXCEL file) paviumTieton_v1.0_vs_swissprot.xlsx.gz
Prunus avium Tieton v1.0 proteins with SwissProt (FASTA file) paviumTieton_v1.0_vs_swissprot_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without SwissProt (FASTA file) paviumTieton_v1.0_vs_swissprot_noHit.fasta.gz
Prunus avium Tieton v1.0 proteins with TrEMBL homologs (EXCEL file) paviumTieton_v1.0_vs_trembl.xlsx.gz
Prunus avium Tieton v1.0 proteins with TrEMBL (FASTA file) paviumTieton_v1.0_vs_trembl_hit.fasta.gz
Prunus avium Tieton v1.0 proteins without TrEMBL (FASTA file) paviumTieton_v1.0_vs_trembl_noHit.fasta.gz

 

Functional annotation for the Prunus avium Tieton genome v1.0 are available for download below. The Prunus avium Tieton 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 paviumTieton_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan paviumTieton_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs paviumTieton_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways paviumTieton_v1.0_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 Prunus avium Tieton 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 avium Tieton_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus avium Tieton_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus avium Tieton_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus avium Tieton_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus avium Tieton_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus avium Tieton_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus avium Tieton_v1.0_rubus_GDR_reftransV2

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 GDR data repository.

The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies.
  • Vanderzande S, Zheng P, Cai L, Barac G, Gasic K, Main D, Iezzoni A and Peace C. The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies. Scientific Reports 10, 7613 (2020). https://doi.org/10.1038/s41598-020-64438-x
Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs wer... [more]
200K Axiom PyrSNP array for Pyrus

Publication

Li X, Singh J, Qin M, Li S, Zhang X, Zhang M, Khan A, Zhang S, Wu J. Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and GWAS in pear (Pyrus). Plant biotechnology journal. 2019 Jan 28.

Description

Pear (Pyrus; 2n = 34), the third most important temperate fruit crop, has great nutritional and economic value. Despite the availability of many genomic resources in pear, it is challenging to genotype novel germplasm resources and breeding progeny... [more]

Resources
Resource Links: 
Search SNPs|https://www.rosaceae.org/tripal_megasearch?datatype=tripal_megasearch_marker
Resource Titles: 
Download
Resource Blocks: 
Download SNP data
File Description File
List of the 200 481 SNP markers that were put on the array.

PBI-17-1582-s007.xlsx
The details of 2388 SNPs mapped on the 17 linkage groups PBI-17-1582-s009.xlsx 
The origin of sequencing 113 pear accessions. PBI-17-1582-s008.xlsx

 

Axiom 70K SNP Array for Pyrus

Publication

Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC genomics. 2019 May 02; 20(1):331.

Description

Background
Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally impor... [more]

Resources
Resource Links: 
View SNPs in JBrowse|https://www.rosaceae.org/jbrowse/index.html?data=data%2Fpyrus%2Fpcommunis_v2.0&loc=Chr1%3A8629257..11947400&tracks=DNA%2Cpc_BartlettDH%2CAxiom_70K_Pear_Genotyping_Array&highlight=
Search SNPs|https://www.rosaceae.org/search/snp_markers
Resource Titles: 
Download
Resource Blocks: 
Download SNP data
File Description File
SNP information for the initial 700K SNPs

tfGDR1035.xlsx
Genome position of 70K SNPs in Pyrus communis Bartlett DH Genome v2.0 pear_70K_genome_pos.xlsx

 

Malus x domestica primary pseudo genome v1.0

Human-Readable NameMalus x domestica primary pseudo genome v1.0
Database NameMalus_x_domestica.v1.0-primary.pseudo.fa
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for Malus_x_domestica.v1.0-primary.pseudo.fa
RegEx/^(\S+).*/
Link-out Typejbrowse
Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution
  • Hardigan Michael A., Feldmann Mitchell J., Lorant Anne, Bird Kevin A., Famula Randi, Acharya Charlotte, Cole Glenn, Edger Patrick P., Knapp Steven J. Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution. Front. Plant Sci., 2020 February 7; 10:1789 | https://doi.org/10.3389/fpls.2019.01789
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid g... [more]