Abstract
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.
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References
Alqudah AM, Samarah NH, Mullen RE (2011) Drought stress effect on crop pollination, seed set, yield and quality. Sustain Agric Rev 6:193–213. doi:10.1007/978-94-007-0186-1_6
Amborella Genome Project (2013) The Amborella genome and the evolution of flowering plants. Science 342. doi: 10.1126/science.1241089
Becker JD, Boavida LC, Carneiro J, Haury M, Feijo J (2003) Transcriptional profiling of Arabidopsis tissues reveals the unique characterictics of the pollen transcriptome. Plant Physiol 133:713–725
Becker JD, Takeda S, Borges F, Dolan L, Feijo JA (2014) Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. BMC Plant Biol 14:197. doi:10.1186/s12870-014-0197-3
Benkert R, Obermeyer G, Bentrup F-W (1997) The turgor pressure of growing lily pollen tubes. Protoplasma 198:1–8
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 252–278
Boavida LC, McCormick S (2007) Temperature as a determinant factor for increased and reproducible in vitro pollen germination in Arabidopsis thaliana. Plant J 52:570–582
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Cheung AY, Wu H-M (2008) Structural and signaling networks for the polar cell growth machinery in pollen tubes. Annu Rev Plant Biol 59:547–572
Du F et al (2014) De novo assembled transcriptome analysis and SSR marker development of a mixture of six tissues from Lilium oriental hybrid ‘Sorbonne’. Plant Mol Biol Rep. doi:10.1007/s11105-014-0746-9
Elias M, Cvrckova F, Obermeyer G, Zarsky V (2001) Microinjection of guanine nucleotide analogues into lily pollen tubes results in isodiametirc tip expansion. Plant Biol 3:489–492
Engel E et al (1997) Immunological and biological properties of Bet v 4, a novel birch pollen allergen with two EF-hand calcium-binding domains. J Biol Chem 272:28630–28637
Fang X, Turner NC, Yan G, Li F, Siddique KHM (2010) Flower numbers, pod production, pollen viability, and pistil function are reduced and flower and pod abortion increased in chickpea (Cicer arietinum L.) under terminal drought stress. J Exp Bot 61:335–345
Feijó JA, Malhó R, Obermeyer G (1995) Ion dynamics and its possible role during in vitro pollen germination and tube growth. Protoplasma 187:155–167
Feijó JA, Sainhas J, Holdaway-Clarke T, Cordeiro S, Kunkel JG, Hepler PK (2001) Cellular oscillations and the regulation of growth: the pollen tube paradigm. Bioessays 23:86–94
Felsenstein J (1989) PHYLIP—phylogeny inference package (version 3.2). Cladistics 5:164–166
Ge W, Song Y, Zhang C, Zhang Y, Burlingame AL, Guo Y (2011) Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen. Biochim Biophys Acta 1814:1964–1973
Grabherr MG et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652
Grobei MA et al (2009) Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. Genome Res 19:1786–1800
Haerizadeh F, Wong CE, Bhalla PL, Gresshoff PM, Singh BP (2009) Genomic expression profiling of mature sybean (Glycine max) pollen. BMC Plant Biol 9:25
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
Hamilton DA, Roy M, Rueda J, Sindhu RK, Sanford J, Mascarenhas JP (1992) Dissection of a pollen-specific promoter from maize by transient transformation assay. Plant Mol Biol 18:211–218
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 52:1043–1058
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
Holdaway-Clarke TL, Feijó JA, Hackett GR, Kunkel JG, Hepler PK (1997) Pollen tube growth and the intracellular cytosolic calcium gradient oscillate in phase while extracellular calcium influx is delayed. Plant Cell 9:1999–2010
Holdaway-Clarke TL, Weddle NM, Kim S, Robi A, Parris C, Kunkel JG, Hepler PK (2003) Effect of extracellular calcium, pH and borate on growth oscillations in Lilium formosanum pollen tubes. J Exp Bot 54:65–72
Holmes-Davies R, Tanaka CK, Vensel WH, Hurkman WJ, McCormick S (2005) Proteome mapping of mature pollen of Arabidopsis thaliana. Proteomics 5:4864–4884
Honys D, Twell D (2003) Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol 132:640–652
Huang J et al (2006) An ankyrin repeat-containing protein, characterized as a ubiquitin ligase, is closely associated with membrane-enclosed organelles and required for pollen germination and pollen tube growth in lily. Plant Physiol 140:1374–1383
Huang J-C, Chang L-C, Wang M-L, Guo C-L, Chung M-C, Jauh G-Y (2011) Identification and exploration of pollen tube small proteins encoded by pollination-induced transcripts. Plant Cell Physiol 52:1546–1559
Konrad K, Wudick MM, Feijo JA (2011) Calcium regulation of tip growth: new genes for old mechanisms. Curr Opin Plant Biol 14:721–730
Lamesch P et al (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210. doi:10.1093/nar/gkr1090
Lang V, Pertl-Obermeyer H, Safiarian MJ, Obermeyer G (2014) Pump up the volume—a central role for the plasma membrane H+ pump in pollen germination and tube growth. Protoplasma 251:477–488
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. doi:10.1186/gb-2009-10-3-r25
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B (2012) RobiNA: a user-friendly, integrated software solution for RNA-seq-based transcriptomics. Nucleic Acids Res 40:W622–W627
Lohse M et al (2014) Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant, Cell Environ 37:1250–1258
Loraine AE, McCormick S, Estrada A, Patel K, Qin P (2013) RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol 162:1092–1109
Messerli M, Danuser G, Robinson KR (1999) Pulsatile influxes of H+, K+ and Ca2+ lag growth pulses of Lilium longiflorum pollen tubes. J Cell Sci 112:1497–1509
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
Michard E, Dias P, Feijo JA (2008) Tobacco pollen tubes as cellular models for ion dynamics: improved spatial and temporal resolution of extracellular flux and free cytosolic concentration of calcium and protons using pHluorin and YC3.1 CaMeleon. Sex Plant Reprod 21:169–181
Michard E, Alves F, Feijo JA (2009) The role of ion fluxes in polarized cell growth and morphogenesis: the pollen tube as an experimental paradigm. Int J Dev Biol 53:1609–1622
Miki-Hiroshige H, Yamanaka Y, Nakamura S, Kurata S, Hirano H (2004) Changes of protein profiles during pollen development in Lilium longiflorum. Sex Plant Reprod 16:209–214
Mouline K et al (2002) Pollen tube development and competitive ability are impaired by disruption of a Shaker K+ channel in Arabidopsis. Genes Dev 16:339–350
Moutinho A, Camacho L, Haley A, Salomé-Pais M, Trewavas A, Malhó R (2001a) Antisense pertubation of protein function in living pollen tubes. Sex Plant Reprod 14:101–104
Moutinho A, Hussey PJ, Trewavas A, Malho R (2001b) cAMP acts as a second messenger in pollen tube growth and reorientation. Proc Natl Acad Sci USA 98:10481–10486
Nobiling R, Reiss H-D (1987) Quatitative analysis of calcium gradients and activity in growing pollen tubes of Lilium longiflorum. Protoplasma 139:20–24
Noir S, Bräutigam A, Colby T, Schmidt J, Panstruga R (2005) A reference map of the Arabidopsis thaliana mature pollen proteome. Biochem Biophys Res Commun 337:1257–1266
Obermeyer G, Kolb H-A (1993) K+ channels in the plasma membrane of lily pollen protoplasts. Bot Acta 106:26–31
Obermeyer G, Weisenseel MH (1991) Calcium channel blocker and calmodulin antagonists affect the gradient of free calcium ions in lily pollen tubes. Eur J Cell Biol 56:319–327
Obermeyer G, Fragner L, Lang V, Weckwerth W (2013) Dynamic adaption of metabolic pathways during germination and growth of lily pollen tubes after inhibition of the electron transport chain. Plant Physiol 162:1822–1833
Okada T, Bhalla PL, Singh MB (2006) Expressed sequence tag analysis of Lilium longiflorum generative cells. Plant Cell Physiol 47:698–705
Okada T, Singh MB, Bhalla PL (2007) Transcriptome profiling of Lilium longiflorum generative cells by cDNA microarray. Plant Cell Rep 26:1045–1052
Okuda S et al (2009) Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells. Nature 458:357–361
Pertl H, Schulze WX, Obermeyer G (2009) The pollen organelle membrane proteome reveals highly spatial-temporal dynamics during germination and tube growth of lily pollen. J Proteome Res 8:5142–5152
Pertl H, Rittmann S, Schulze WX, Obermeyer G (2011) Identification of lily pollen 14-3-3 isoforms and their subcellular and time-dependent expression profile. Biol Chem 392:249–262
Pertl-Obermeyer H, Obermeyer G (2014) Pollen cultivation and preparation for proteomic studies. In: Jorrin-Novo JV, Komatsu S, Weckwerth W, Winkoop S (eds) Plant proteomics: methods and protocols. Methods in molecular biology, vol 1072. Springer, New York, pp 435–449
Pina C, Pinto F, Feijo JA, Becker JD (2005) Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, divison control and gene expression regulation. Plant Physiol 138:744–756
Potocky M, Jones MA, Bezvoda R, Smirnoff N, Zarsky V (2007) Reactive oxigen species produced by NADPH oxidase are involved in pollen tube growth. New Phytol 174:742–751
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
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140
Rodriguez-Enriquez MJ, Mehdi S, Dickinson HG, Grant-Downton RT (2013) A novel method for efficient in vitro germination and tube growth of Arabidopsis thaliana pollen. New Phytol 197:668–679
Rosen WG, Gawlik SR, Dashek WV, Siegesmund KA (1964) Fine structure and cytochemistry of Lilium pollen tubes. Am J Bot 51:61–71
Sangha JS, Gu K, Kaur J, Yin Z (2010) An improved method for RNAisolation and cDNA library construction from immature seeds of Jatropha curcas L. BMC Res Notes 3:126. doi:10.1186/1756-0500-3-126
Shahin A, van Kaauwen M, Esselink D, Bargsten JW, van Tuyl JM, Visser RGF, Arens P (2012) Generation and analysis of expressed sequence tags in the extreme large genomes of Lilium and Tulipa. BMC Genomics 13:640. doi:10.1186/1471-2164-13-640
Soto G, Alleva K, Mazella MA, Amodeo G, Muschietti JP (2008) AtTIP1;3 and AtTIP5;1, the only highly expressed Arabidopsis pollen-specific aquaporins, transport water and urea. FEBS Lett 582:4077–4082
Steinhorst L, Kudla J (2013) Calcium—a central regulator of pollen germination and tube growth. Biochim Biophys Acta 1833:1573–1581
Strickler SR, Bombarely A, Mueller LA (2012) Designing a transcriptome next-generation sequencing project for nonmodel plant species. Am J Bot 99:1–10
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Thimm O et al (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939
Thomas SG, Franklin-Tong VE (2004) Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429:305–309
Usadel B et al (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol 138:1195–1204
Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eisenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, maize. Plant, Cell Environ 32:1211–1229
vander Woude WJ, Morre DJ, Bracker CE (1971) Isolation and characterisation of secretory vesicels in germinated pollen of Lilium longiflorum. J Cell Sci 8:331–351
Wang H, Jiang L (2011) Transient expression and analysis of fluorescent reporter proteins in plant pollen tubes. Nat Protoc 6:419–426
Wang Y, Zhang W-Z, Song L-F, Zou J-J, Su Z, Wu W-H (2008) Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol 148:1201–1211
Ward JA, Ponnala L, Weber CA (2012) Strategies for transcriptome analysis in nonmodel plants. Am J Bot 99:267–276
Wei LQ, Xu WY, Deng ZY, Su Z, Xue Y, Wang T (2010) Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa. BMC Genom 11:338
Weisenseel MH, Nuccitelli R, Jaffe LA (1975) Large electrical currents traverse growing pollen tubes. J Cell Biol 66:556–567
Wu J, Wang S, Gu Y, Zhang S, Publicover SJ, Franklin-Tong VE (2011) Self-incompatibility in Papaver rhoeas activates nonspecific cation conductance permeable to Ca2+ and K+. Plant Physiol 155:963–973
Yokota E, Shimmen T (1994) Isolation and characterization of plant myosin from pollen tubes of lily. Protoplasma 177:153–162
Yokota E, Takahara K, Shimmen T (1998) Actin-bundling protein isolated from pollen tubes of lily. Biochemical and immunocytochemical characterization. Plant Physiol 116:1421–1429
Zhou J, Song L-F, Zhang W, Wang Y, Ruan S, Wu W-H (2009) Comparative proteomic analysis of Arabidopsis mature pollen and germinated pollen. J Integr Plant Biol 51:438–455
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136:2621–2632
Acknowledgments
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.
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Lang, V., Usadel, B. & Obermeyer, G. De novo sequencing and analysis of the lily pollen transcriptome: an open access data source for an orphan plant species. Plant Mol Biol 87, 69–80 (2015). https://doi.org/10.1007/s11103-014-0261-2
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DOI: https://doi.org/10.1007/s11103-014-0261-2