Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 506486
Title Elucidating and mining the Tulipa and Lilium transcriptomes
Author(s) Moreno-Pachon, N.M.; Leeggangers, Melissa; Nijveen, Harm; Severing, Edouard; Hilhorst, Henk; Immink, Richard G.H.
Source Plant Molecular Biology 92 (2016)3. - ISSN 0167-4412 - p. 249 - 261.
DOI http://dx.doi.org/10.1007/s11103-016-0508-1
Department(s) Laboratory of Plant Physiology
Bioinformatics
EPS
PRI BIOS Plant Development Systems
Publication type Refereed Article in a scientific journal
Publication year 2016
Keyword(s) De novo assembly - Genes - Lily (Lilium sp) - Sequencing - Transcriptome browser - Tulip (Tulip sp)
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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