• R. Salinas, Natalia & Zurn, Jason & Mathey, Megan & Mookerjee, Sonali & Denoyes, Béatrice & Perrotte, Justine & Potier, Aline & Finn, Chad & Hancock, James & Stewart, Philip & Bassil, Nahla. (2017). Validation of molecular markers associated with perpetual flowering in Octoploid Fragaria germplasm. Molecular Breeding. 37. 70. DOI: 10.1007/s11032-017-0672-2.
Perpetual-flowering (PF) is a highly desirable trait within cultivated strawberries (Fragaria texttimesananassa) for the commercial and home garden markets. The most widely used source of the PF trait was originally introgressed from a wild F. virginiana subsp. glauca accession collected in the Wasatch Mountains near Salt Lake City, UT in 1955. This source is conferred by a single dominant QTL, FaPFRU, and was recently identified in multiple bi-p... [more]

Malus x domestica HFTH1 Genome v1.0.a1 proteins

Human-Readable NameMalus x domestica HFTH1 Genome v1.0.a1 proteins
Database NameMalus_x_domestica_HFTH1_v1.0.a1.proteins.fasta
Database Typeprotein
FASTA Header Formatdefault
External DatabaseJBrowse for Malus x domestica HFTH1 v1.0.a1 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

Malus x domestica HFTH1 Genome v1.0.a1 transcripts

Human-Readable NameMalus x domestica HFTH1 Genome v1.0.a1 transcripts
Database NameMalus_x_domestica_HFTH1_v1.0.a1.transcripts.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseGDR
RegEx/^(\S+).*/
Link-out Typelink

Malus x domestica HFTH1 Genome v1.0.a1 chromosomes

Human-Readable NameMalus x domestica HFTH1 Genome v1.0.a1 chromosomes
Database NameMalus_x_domestica_HFTH1_v1.0.a1.genome.fasta
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for Malus x domestica HFTH1 v1.0.a1 genome
RegEx/^(\S+).*/
Link-out Typejbrowse

Publication

Liyi Zhang, Jiang Hu, Xiaolei Han, Jingjing Li , Yuan Gao, Christopher M. Richards , Caixia Zhang, Yi Tian, Guiming Liu, Hera Gul, Dajiang Wang, Yu Tian, Chuanxin Yang, Minghui Meng, Gaopeng Yuan, Guodong Kang, Yonglong Wu, Kun Wang, Hengtao Zhang, Depeng Wang & Peihua Cong. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature communications. 2019 April 02.

 

About the Assembl... [more]

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

Downloads

Chromosome(FASTA file) Malus_x_domestica_HFTH1_v1.0.a1.fasta.gz

 

The Malus x domestica HFTH1 v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Transcript CDS sequences (FASTA file) Malus_x_domestica_HFTH1_v1.0.a1.transcripts.fasta.gz
Protein sequences  (FASTA file) Malus_x_domestica_HFTH1_v1.0.a1.proteins.fasta.gz
Genes (GFF3 file) Malus_x_domestica_HFTH1_v1.0.genes.a1.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.

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 Malus x domestica 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 Malus_x_domestica_HFTH1_v1.0.a1_f.x.ananassa_GDR_reftransV1
Malus x domestica GDR RefTrans v1 Malus_x_domestica_HFTH1_v1.0.a1_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Malus_x_domestica_HFTH1_v1.0.a1_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Malus_x_domestica_HFTH1_v1.0.a1_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Malus_x_domestica_HFTH1_v1.0.a1_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Malus_x_domestica_HFTH1_v1.0.a1_rubus_GDR_reftransV2

Functional annotation for the Malus x domestica HFTH1 genome v1.0 are available for download below. The Malus x domestica HFTH1 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 Malus_x_domestica_HFTH1_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Malus_x_domestica_HFTH1_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Malus_x_domestica_HFTH1_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Malus_x_domestica_HFTH1_v1.0_KEGG-pathways.xlsx.gz

 

Homology of the Malus x domestica HFTH1 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 (TAIR10), 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

Malus x domestica HFTH1 v1.0 proteins with NCBI nr homologs (EXCEL file) Mxd_HFTH1_v1.0_vs_nr.xlsx.gz
Malus x domestica HFTH1 v1.0 proteins with NCBI nr (FASTA file) Mxd_HFTH1_v1.0_vs_nr_hit.fasta.gz
Malus x domestica HFTH1 v1.0 proteins without NCBI nr (FASTA file) Mxd_HFTH1_v1.0_vs_nr_noHit.fasta.gz
Malus x domestica HFTH1 v1.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) Mxd_HFTH1_v1.0_vs_arabidopsis.xlsx.gz
Malus x domestica HFTH1 v1.0 proteins with arabidopsis (TAIR10) (FASTA file) Mxd_HFTH1_v1.0_vs_arabidopsis_hit.fasta.gz
Malus x domestica HFTH1 v1.0 proteins without arabidopsis (TAIR10) (FASTA file) Mxd_HFTH1_v1.0_vs_arabidopsis_noHit.fasta.gz
Malus x domestica HFTH1 v1.0 proteins with SwissProt homologs (EXCEL file) Mxd_HFTH1_v1.0_vs_swissprot.xlsx.gz
Malus x domestica HFTH1 v1.0 proteins with SwissProt (FASTA file) Mxd_HFTH1_v1.0_vs_swissprot_hit.fasta.gz
Malus x domestica HFTH1 v1.0 proteins without SwissProt (FASTA file) Mxd_HFTH1_v1.0_vs_swissprot_noHit.fasta.gz
Malus x domestica HFTH1 v1.0 proteins with TrEMBL homologs (EXCEL file) Mxd_HFTH1_v1.0_vs_trembl.xlsx.gz
Malus x domestica HFTH1 v1.0 proteins with TrEMBL (FASTA file) Mxd_HFTH1_v1.0_vs_trembl_hit.fasta.gz
Malus x domestica HFTH1 v1.0 proteins without TrEMBL (FASTA file) Mxd_HFTH1_v1.0_vs_trembl_noHit.fasta.gz

 

The Rubus idaeus cv. Heritage (red raspberry) transcriptomic data hosted by the Genome Database for Rosaceae (GDR) was compiled and analyzed by Centro Regional de Estudios en Alimentos Saludables-CREAS and the Centro de Modelamiento Matemático (CMM) at Universidad de Chile. The goal of this project was to evaluate the molecular changes during raspberry ripening and isolate the differential expressed genes (DEGs) associated with the fruit development of this economically valuable crop. The specific objectives of the DEGs data generation were to:

1. Develop a sequence database for DEGs during Raspberry development;

2. Id... [more]

Resource Titles: 
Publications
Download
Resource Blocks: 

More information about the Transcriptomic data can be found in the publication:

Travisany D., Ayala-Raso A., Di-Genova A., Monsalve A., Bernales A., Martínez J.P., González-Agüero M., Defilippi B., Cherian S., Maass A., Fuentes 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, 254 26-34

Bernales M., Monsalve L., Ayala-Raso A., Valdenegro M., Martínez J.P., Travisany D., Defilippi B., González-Agüero M., Cherian S., Fuentes L., Expression of two indole-3-acetic acid (IAA)-amido synthetases (GH3) genes during fruit development and ripening of raspberry (Rubus idaeus Heritage). Sci. Hort. 246, 2019, 168-175.

Fuentes L, Monsalve L, Morales-Quintana L, Valdenegro M, Martínez JP, Defilippi BG, González-Agüero M. Differential expression of ethylene biosynthesis genes in drupelets and receptacle of raspberry (Rubus idaeus). J. Plant Physiol. 2015 May 1; 179:100-5. doi: 10.1016/j.jplph.2015.02.005. 

 Available Files
 Rubus idaeus Heritage transcripts v1 Rubus_idaeus_heritage_sequences_GDr_20180225_1145-LFV.fasta