Elucidating and mining the Tulipa and Lilium transcriptomes

N.M. Moreno-Pachon, Melissa Leeggangers, Harm Nijveen, Edouard Severing, Henk Hilhorst, Richard G.H. Immink*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Abstract

Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser (http://www.bioinformatics.nl/bulbs/db/species/index). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.

Original languageEnglish
Pages (from-to)249-261
JournalPlant Molecular Biology
Volume92
Issue number3
DOIs
Publication statusPublished - 2016

Fingerprint

Tulipa
Lilium
Transcriptome
transcriptome
Genome
genome
Transcription Factors
transcription factors
Data Mining
repetitive sequences
Nucleic Acid Repetitive Sequences
Genomics
Computational Biology
bioinformatics
bulbs
Noise
RNA
genomics

Keywords

  • De novo assembly
  • Genes
  • Lily (Lilium sp)
  • Sequencing
  • Transcriptome browser
  • Tulip (Tulip sp)

Cite this

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title = "Elucidating and mining the Tulipa and Lilium transcriptomes",
abstract = "Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser (http://www.bioinformatics.nl/bulbs/db/species/index). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.",
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Elucidating and mining the Tulipa and Lilium transcriptomes. / Moreno-Pachon, N.M.; Leeggangers, Melissa; Nijveen, Harm; Severing, Edouard; Hilhorst, Henk; Immink, Richard G.H.

In: Plant Molecular Biology, Vol. 92, No. 3, 2016, p. 249-261.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Elucidating and mining the Tulipa and Lilium transcriptomes

AU - Moreno-Pachon, N.M.

AU - Leeggangers, Melissa

AU - Nijveen, Harm

AU - Severing, Edouard

AU - Hilhorst, Henk

AU - Immink, Richard G.H.

PY - 2016

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N2 - Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser (http://www.bioinformatics.nl/bulbs/db/species/index). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.

AB - Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser (http://www.bioinformatics.nl/bulbs/db/species/index). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.

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KW - Genes

KW - Lily (Lilium sp)

KW - Sequencing

KW - Transcriptome browser

KW - Tulip (Tulip sp)

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JO - Plant Molecular Biology

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