Rose transcriptome and WagRhSNP 68K Axiom SNP array (Koning-Boucoiran et al. 2015)

Analysis NameRose transcriptome and WagRhSNP 68K Axiom SNP array (Koning-Boucoiran et al. 2015)
MethodTrinity, iAssembler (v1.3.2) pipeline, the CLC assembler
SourceRNA-Seq data from tetraploid cut, garden roses and diploid Rosa multiflora
Date performed2015-01-28

In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.


Koning-boucoiran CF, Esselink GD, Vukosavljev M, Van_t_westende WP, Gitonga VW, Krens FA, Voorrips RE, Van_de_weg WE, Schulz D, Debener T, Arens P and Smulders M(2015) Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.). Front. Plant Sci. 6:249.

Download SNP and transcriptome data
File Description File
The complete description of all SNPs on the WagRhSNP array rose_transcriptome_table 2.csv
Orthologous ORF sequences of roses, constructed using the orthology-guided assembly procedure rose_transcriptome_table 3.csv
InterPro predictions for the orthologous transcripts of cut and garden roses. rose_transcriptome_table 4.csv
GO classes and GO annotations of the Rh-Fv transcripts.  rose_transcriptome_table 5.csv
Key from ROSASeq transcripts to Rh_Fv_orthologs rose_transcriptome_table 6.csv