title: Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs.
abstract: BACKGROUND
  Vernalization is an obligatory requirement of extended exposure to low temperatures to induce flowering in certain plants. It is the most important factor affecting flowering time and quality in Easter lily (Lilium longiflorum). Exposing the bulbs to 4 °C gradually decreases flowering time up to 50% compared to non-vernalized plants. We aim to understand the molecular regulation of vernalization in Easter lily, for which we characterized the global expression in lily bulb meristems after 0, 2, 5, 7 and 9 weeks of incubation at 4 °C.
  
  
  RESULTS
  We assembled de-novo a transcriptome which, after filtering, yielded 121,572 transcripts and 42,430 genes which hold 15,414 annotated genes, with up to 3,657 GO terms. This extensive annotation was mapped to the more general GO slim plant with a total of 94 terms. The response to cold exposure was summarized in 6 expression clusters, providing useful patterns for dissecting the dynamics of vernalization in lily. The functional annotation (GO and GO slim plant) was used to group transcripts in gene sets. Analysis of these gene sets and profiles revealed that most of the enriched functions among genes up-regulated by cold exposure were related to epigenetic processes and chromatin remodeling. Candidate vernalization genes in lily were selected based on their sequence similarity to known regulators of flowering in other species.
  
  
  CONCLUSIONS
  We present a detailed analysis of gene expression dynamics during vernalization in Lilium, covering several time points and accounting for biological variation by the use of replicates. The resulting collection of transcripts and novel isoforms provides a useful resource for studying the changes occurring during vernalization at a fine level. The selected potential candidate genes can shed light on the regulation of this process.
authors.affiliation: Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands. c.villacorta@genetwister.nl.
authors.forename: Carlos
authors.initials: C
authors.lastname: Villacorta-Martin
authors.affiliation: Department of Life Sciences, Ben Gurion University of the Negev, P.O. Box 653, Beersheva, 84105, Israel. ffnunezdcgo@conacyt.mx.|Present address: Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Tulancingo Km. 4.5, C. P. 42184, Mineral de la Reforma, Hidalgo, Mexico. ffnunezdcgo@conacyt.mx.
authors.forename: Francisco F
authors.initials: FF
authors.lastname: Núñez de Cáceres González
authors.affiliation: Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands. J.R.deHaan@genetwister.nl.
authors.forename: Jorn
authors.initials: J
authors.lastname: de Haan
authors.affiliation: Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands. k.m.j.huijben@genetwister.nl.
authors.forename: Kitty
authors.initials: K
authors.lastname: Huijben
authors.affiliation: Genetwister Technologies B.V., P.O. Box 193, NL6700 AD, Wageningen, The Netherlands. p.passarinho@genetwister.nl.
authors.forename: Paul
authors.initials: P
authors.lastname: Passarinho
authors.affiliation: Department of Life Sciences, Ben Gurion University of the Negev, P.O. Box 653, Beersheva, 84105, Israel. lugassim@gmail.com.
authors.forename: Maya
authors.initials: M
authors.lastname: Lugassi-Ben Hamo
authors.affiliation: Department of Life Sciences, Ben Gurion University of the Negev, P.O. Box 653, Beersheva, 84105, Israel. mzaccai@bgu.ac.il.
authors.forename: Michele
authors.initials: M
authors.lastname: Zaccai
mesh_terms: D003080:Cold Temperature; D044127:Epigenesis, Genetic; D035264:Flowers / Q000235:genetics / Q000254:growth & development*; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D027762:Lilium / Q000235:genetics* / Q000502:physiology; D058977:Molecular Sequence Annotation