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Whole transcriptome profiling of the vernalization process in Lilium longiflorum bulbs

ABSTRACT: Whole transcriptome profiling of the vernalization process in Lilium longiflorum bulbs

PROVIDER: PRJEB6959 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR578452_1.fastq.gz	Fastqsanger.gz
	ERR578452_2.fastq.gz	Fastqsanger.gz
	ERR578453_1.fastq.gz	Fastqsanger.gz
	ERR578453_2.fastq.gz	Fastqsanger.gz
	ERR578454_1.fastq.gz	Fastqsanger.gz

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Whole transcriptome profiling of the vernalization process in Lilium longiflorum bulbs

Project description:We used high throughput sequencing of coding RNA to identify systematic patterns of expression during vernalization in meristems of lily bulbs that were treated with cold temperature for increasing periods of time. cDNA libraries were constructed from bulbs stored at 25 degrees Celsius (control) and at 4 degrees Celsius for 2, 5, 7 and 9 weeks

2015-03-17 | E-MTAB-2825 | biostudies-arrayexpress

Lilium longiflorum

Project description:Lilium longiflorum overview

| PRJNA108727 | ENA

Lilium longiflorum

Project description:Lilium longiflorum Raw sequence reads

| PRJNA1000239 | ENA

Lilium longiflorum

Project description:Lilium longiflorum Transcriptome or Gene expression

| PRJNA92295 | ENA

Lilium longiflorum

Project description:RNA-sequencing of mature pollen and isolated generative cell in Lilium longiflorum

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

Project description: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.

| S-EPMC4515921 | biostudies-literature

Lilium longiflorum

Project description:Transcriptiome Analysis by RNA-Seq Reveals Genes Related to Heterosis in Lilium longiflorum

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Lilium longiflorum strain:White Heaven

Project description:Lilium longiflorum strain:White Heaven Transcriptome or Gene expression

| PRJNA259918 | ENA

Lilium

Project description:Lilium longiflorum, Lilium formolongi, Transcriptome

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Genotyping by high throughput sequencing of four different cultivars of Lilium

Project description:The cDNA of 4 Lilium cultivars were sequenced in this study in order to develop SNP markers for mapping purpose. The four selected cultivars represent the four main hybrid groups in Lilium which are (Asiatic, Oriental, Longiflorum, and Trumpet). The SNP markers developed of this study will be implemented in mapping and association studies that aims to find SNP markers linked to virus resistance in Lilium. To achieve this target, SNP markers were generated from each cultivar separately, and of the four cultivars together trying to cover as much as variation in each cultivar and also to find SNP markers that can distinguish the four cultivars. Doing so, we hope to identify different genes resistance to virus in the four hybrid groups of Lilium.

2013-01-17 | E-MTAB-840 | biostudies-arrayexpress

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