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 language | English |
|---|---|
| Pages (from-to) | 249-261 |
| Journal | Plant Molecular Biology |
| Volume | 92 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - 2016 |
Fingerprint
Keywords
- De novo assembly
- Genes
- Lily (Lilium sp)
- Sequencing
- Transcriptome browser
- Tulip (Tulip sp)
Cite this
}
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 journal › Article › Academic › peer-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
Y1 - 2016
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.
KW - De novo assembly
KW - Genes
KW - Lily (Lilium sp)
KW - Sequencing
KW - Transcriptome browser
KW - Tulip (Tulip sp)
U2 - 10.1007/s11103-016-0508-1
DO - 10.1007/s11103-016-0508-1
M3 - Article
VL - 92
SP - 249
EP - 261
JO - Plant Molecular Biology
JF - Plant Molecular Biology
SN - 0167-4412
IS - 3
ER -