De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species
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Pollen grains of Lilium longiflorum are a long-established model system for pollen germination and tube tip growth. Due to their size, protein content and almost synchronous germination in synthetic media, they provide a simple system for physiological measurements as well as sufficient material for biochemical studies like protein purifications, enzyme assays, organelle isolation or determination of metabolites during germination and pollen tube elongation. Despite recent progresses in molecular biology techniques, sequence information of expressed proteins or transcripts in lily pollen is still scarce. Using a next generation sequencing strategy (RNAseq), the lily pollen transcriptome was investigated resulting in more than 50 million high quality reads with a length of 90 base pairs. Sequenced transcripts were assembled and annotated, and finally visualized with MAPMAN software tools and compared with other RNAseq or genome data including Arabidopsis pollen, Lilium vegetative tissues and the Amborella trichopoda genome. All lily pollen sequence data are provided as open access files with suitable tools to search sequences of interest.
KeywordsLilium longiflorum Next generation sequencing Pollen RNA-Seq Tip growth
The project was partially financed by the Austrian Science Fund (FWF grant no. P21298), the Stiftungs- und Fördergesellschaft of the Univ. Salzburg and by the University priority program “BioScience and Health”. BU thanks the BMBF for funding through the primary database FKZ 0315961 and the state NRW–BioSC for the project PNP-Express. We thank Professors Dr. Zhongshan Gao, Dept. Horticulture, Zhejiang Univ., China, and Dr. Paul Arens, Wageningen Univ., The Netherlands, for providing data of the RNAseq study on Lilium oriental hybrid tissue and on L. longiflorum leaf tissue, respectively.
- Amborella Genome Project (2013) The Amborella genome and the evolution of flowering plants. Science 342. doi: 10.1126/science.1241089
- Bibikova TN, Assmann S, Gilroy S (2004) Ca2+ and pH as integrated signals in transport control. In: Blatt MR (ed) Membrane transport in plants. Annual Plant Review, vol 15. Blackwell, Oxford, pp 252–278Google Scholar
- Felsenstein J (1989) PHYLIP—phylogeny inference package (version 3.2). Cladistics 5:164–166Google Scholar
- Hafidh S, Breznenova K, Ruzicka P, Fecikova J, Capkova V, Honys D (2012) Comprehensive analysis of tobacco pollen transcriptome unveils common pathways in polar cell expansion and underlying heterochronic shift during spermatogenesis. BMC Plant Biol 12:24. doi: 10.1186/1471-2229-12-24 PubMedCentralPubMedCrossRefGoogle Scholar
- Han B, Chen S, Dai S, Yang N, Wang T (2010) Isobaric tags for relative and absolute quantification-based comparative proteomics reveals the features of plasma membrane-associated proteomes of pollen grains and pollen tubes from Lilium davidii. J Integr Plant Biol 52:1043–1058PubMedCrossRefGoogle Scholar
- Hartmann S, Vision TJ (2008) Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol 26. doi: 10.1186/1471-2148-8-95
- Michalski A et al (2011) Mass spectrometry-based proteomics using Q exactive, a high-performance benchtop quadrupole orbitrap mass spectrometer. Mol Cell Proteomics 10. doi: 10.1074/mcp.M111.011015-1
- Qin Y et al (2009) Penetration of the stigma and style elicits a novel transcriptome in pollen tubes, pointing to genes critical for growth in a pistil. PLoS Genetics 5. doi: 10.1371/journal.pgen.1000621
- vander Woude WJ, Morre DJ, Bracker CE (1971) Isolation and characterisation of secretory vesicels in germinated pollen of Lilium longiflorum. J Cell Sci 8:331–351Google Scholar