Whole transcriptome profiling of the vernalization process in Lilium longiflorum (cultivar White Heaven) bulbs

Abstract

BackgroundVernalization 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1675-1) contains supplementary material, which is available to authorized users.

Mechanisms of vegetative propagation in bulbs : a molecular approach

“…Although in other bulbous studies filtering out low abundant sequences reduced significantly the number of predicted genes to a level that gets close to what is reported for model species (Villacorta-Martin et al 2015), we proved that in our data this filtering reduced dramatically the percentage of transcripts with substantial homology to a known plant gene. Therefore, our nonfiltered transcriptomes may not reflect the true number of genes but they rather represent extensive transcriptome coverage for both tulip and lily.…”

“…focused on sequencing the transcriptome of leaves (Wang et al 2014), bulblets (Li et al 2014b) and meristem-enriched tissue (Villacorta- Martin et al 2015) of different Lilium cultivars, using the Illumina HiSeq sequencing platform. These studies resulted in the identification of 37,843 unigenes for leaves (Wang et al 2014), 52,901 unigenes in bulblets (Li et al 2014b) and 42,430 genes for the meristem-enriched lily tissues (Villacorta- Martin et al 2015).…”

Virus-induced gene silencing (VIGS) in <i>Lilium leichtlinii</i> using the <i>Cucumber mosaic virus</i> vector

“…An abundance of Lilium gene sequences have been identified via NGS in an effort to characterize agriculturally important traits Villacorta-Martin et al 2015;Wang et al 2014), and as a result, the establishment of reversegenetics tools is an urgent issue for the functional characterization of the identified sequences. Because VIGS is able to alter plant phenotypes in relatively short periods of time and allows researchers to characterize phenotypes that might be lethal in stable transgenic plants, the technique should be valuable for the functional screening of expressed sequences.…”

“…Several genes involved in anthocyanin and carotenoid biosyntheses have been studied in lilies (Jeknić et al 2012;Lai et al 2012;Nakatsuka et al 2003Nakatsuka et al , 2009Yamagishi et al 2010aYamagishi et al , 2010b. Recently, the transcriptomes of several lily organs have been sequenced using next-generation sequencing (NGS), and a variety of potentially important novel genes have been identified Villacorta-Martin et al 2015;Wang et al 2014), although their specific functions remain to be determined.…”

The hot, the cold and the tulip : the regulation of flowering time and dormancy release

“…Though, a better understanding of the genetic and molecular mechanisms underlying the developmental response of a tulip to temperature is essential to create 'climate-proof' tulips in the future. In contrast to the lack of knowledge on flowering time control and dormancy in tulips, some information is available from other bulbous species, such as lily (Villacorta-Martin et al, 2015) and detailed insights have been obtained from studying model dicot and monocot species (Capovilla et al, 2014;Shrestha et al, 2014;Blümel et al, 2015). …”