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.)

C.F.S. Koning, G. Esselink, M. Vukosavljev, W.P.C. van 't Westende, V.W. Gitonga, F.A. Krens, R.E. Voorrips, W.E. van de Weg, D. Schulz, T. Debener, C.A. Maliepaard, P.F.P. Arens, M.J.M. Smulders

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Abstract

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.
Original languageEnglish
Article number249
Number of pages10
JournalFrontiers in Plant Science
Volume6
DOIs
Publication statusPublished - 2015

Fingerprint

transcriptome
single nucleotide polymorphism
Rosa
RNA
genes
tetraploidy
gardens
germplasm
Rosa multiflora
RNA libraries
Fragaria vesca
Rosaceae
genotyping
strawberries
chromosome mapping
diploidy
genetic markers
genome
breeding

Keywords

  • powdery mildew
  • markers
  • tool
  • identification
  • resistance
  • genome
  • diversity
  • sequences
  • platform
  • plant

Cite this

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title = "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.)",
abstract = "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.",
keywords = "powdery mildew, markers, tool, identification, resistance, genome, diversity, sequences, platform, plant",
author = "C.F.S. Koning and G. Esselink and M. Vukosavljev and {van 't Westende}, W.P.C. and V.W. Gitonga and F.A. Krens and R.E. Voorrips and {van de Weg}, W.E. and D. Schulz and T. Debener and C.A. Maliepaard and P.F.P. Arens and M.J.M. Smulders",
year = "2015",
doi = "10.3389/fpls.2015.00249",
language = "English",
volume = "6",
journal = "Frontiers in Plant Science",
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publisher = "Frontiers",

}

TY - JOUR

T1 - 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.)

AU - Koning, C.F.S.

AU - Esselink, G.

AU - Vukosavljev, M.

AU - van 't Westende, W.P.C.

AU - Gitonga, V.W.

AU - Krens, F.A.

AU - Voorrips, R.E.

AU - van de Weg, W.E.

AU - Schulz, D.

AU - Debener, T.

AU - Maliepaard, C.A.

AU - Arens, P.F.P.

AU - Smulders, M.J.M.

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

KW - powdery mildew

KW - markers

KW - tool

KW - identification

KW - resistance

KW - genome

KW - diversity

KW - sequences

KW - platform

KW - plant

U2 - 10.3389/fpls.2015.00249

DO - 10.3389/fpls.2015.00249

M3 - Article

VL - 6

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

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ER -