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.
authors.affiliation: Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands.
authors.forename: Natalia M
authors.initials: NM
authors.lastname: Moreno-Pachon
authors.affiliation: Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands.
authors.forename: Hendrika A C F
authors.initials: HA
authors.lastname: Leeggangers
authors.affiliation: Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands.|Laboratory of Bioinformatics, Wageningen University, Wageningen, Netherlands.
authors.forename: Harm
authors.initials: H
authors.lastname: Nijveen
authors.affiliation: Laboratory of Bioinformatics, Wageningen University, Wageningen, Netherlands.|Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
authors.forename: Edouard
authors.initials: E
authors.lastname: Severing
authors.affiliation: Wageningen Seed Laboratory (WSL), Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.
authors.forename: Henk
authors.initials: H
authors.lastname: Hilhorst
authors.affiliation: Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands. richard.immink@wur.nl.
authors.forename: Richard G H
authors.initials: RG
authors.lastname: Immink
mesh_terms: D059014:High-Throughput Nucleotide Sequencing; D027762:Lilium / Q000235:genetics*; D017422:Sequence Analysis, DNA; D059467:Transcriptome / Q000235:genetics*; D031447:Tulipa / Q000235:genetics*
keywords: De novo assembly; Genes; Lily (Lilium sp); Sequencing; Transcriptome browser; Tulip (Tulip sp)