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.)

Research output: Contribution to journalArticleResearchpeer review

Authors

  • Carole F.S. Koning-Boucoiran
  • G. Danny Esselink
  • Mirjana Vukosavijev
  • Wendy P.C. Van’T Westende
  • Virginia W. Gitonga
  • Frans A. Krens
  • Roeland E. Voorrips
  • W. Eric Van De Weg
  • Dietmar Schulz
  • Thomas Debener
  • Chris Maliepaard
  • Paul Arens
  • Marinus J.M. Smulders

Research Organisations

External Research Organisations

  • Wageningen University and Research
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Details

Original languageEnglish
Article number249
Pages (from-to)1-10
Number of pages10
JournalFrontiers in Plant Science
Volume6
Issue numberAPR
Publication statusPublished - 21 Apr 2015

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 muitiflora 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

    Assembly, EST, Genotyping, Rosa, SNP array, Transcriptomics

ASJC Scopus subject areas

Cite this

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.). / Koning-Boucoiran, Carole F.S.; Danny Esselink, G.; Vukosavijev, Mirjana et al.
In: Frontiers in Plant Science, Vol. 6, No. APR, 249, 21.04.2015, p. 1-10.

Research output: Contribution to journalArticleResearchpeer review

Koning-Boucoiran, CFS, Danny Esselink, G, Vukosavijev, M, Van’T Westende, WPC, Gitonga, VW, Krens, FA, Voorrips, RE, Van De Weg, WE, Schulz, D, Debener, T, Maliepaard, C, Arens, P & Smulders, MJM 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.)', Frontiers in Plant Science, vol. 6, no. APR, 249, pp. 1-10. https://doi.org/10.3389/fpls.2015.00249
Koning-Boucoiran, C. F. S., Danny Esselink, G., Vukosavijev, M., Van’T Westende, W. P. C., Gitonga, V. W., Krens, F. A., Voorrips, R. E., Van De Weg, W. E., Schulz, D., Debener, T., Maliepaard, C., Arens, P., & Smulders, M. J. 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.). Frontiers in Plant Science, 6(APR), 1-10. Article 249. https://doi.org/10.3389/fpls.2015.00249
Koning-Boucoiran CFS, Danny Esselink G, Vukosavijev M, Van’T Westende WPC, Gitonga VW, Krens FA et al. 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.). Frontiers in Plant Science. 2015 Apr 21;6(APR):1-10. 249. doi: 10.3389/fpls.2015.00249
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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 muitiflora 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.",
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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-Boucoiran, Carole F.S.

AU - Danny Esselink, G.

AU - Vukosavijev, Mirjana

AU - Van’T Westende, Wendy P.C.

AU - Gitonga, Virginia W.

AU - Krens, Frans A.

AU - Voorrips, Roeland E.

AU - Van De Weg, W. Eric

AU - Schulz, Dietmar

AU - Debener, Thomas

AU - Maliepaard, Chris

AU - Arens, Paul

AU - Smulders, Marinus J.M.

N1 - Publisher Copyright: © 2015 Koning-Boucoiran, Esselink, Vukosavljev, van ’t Westende, Gitonga, Krens, Voorrips, van de Weg, Schulz, Debener, Maliepaard, Arens and Smulders..

PY - 2015/4/21

Y1 - 2015/4/21

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 muitiflora 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.

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KW - EST

KW - Genotyping

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JO - Frontiers in Plant Science

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