Transcriptomic analysis of Asiatic lily in the process of vernalization via RNA-seq

Abstract

The new transcriptomes provided comprehensive sequence profiling data of transcriptomic variation during vernalization in Lily Asiatic Hybrids 'Tiny ghost'. A number of 52,277,184 sequencing raw reads totaling 5.11 Gbp of the chilling treatment (4 °C) sample and 39,466,176 sequencing raw reads totaling 3.85 Gbp of room temperature control (25 °C) sample were assembled de novo into 68,718 unigenes with a mean length of 984 bp, and a total of 33,208 (45.6%) unigenes were annotated by using public protein databases with a cut-off E value about 10(-5). There are 6,153 unigenes of which were assigned to specific metabolic pathways by the Kyoto encyclopedia of genes and genomes. Gene Ontology analysis of the annotated unigenes revealed that the majority of sequenced genes were associated with signal transduction mechanisms, posttranslational modification, protein turnover and chaperones. In addition, the genes expression levels were compared just after vernalization completion between the cold treatment and room temperature control. There are 68,116 unigenes were differentially expressed, and hierarchical clustering analysis arranged 7,301 significantly differentially-expressed unigenes into 56 groups. Six genes related to the vernalization were selected to confirm their expression levels by using quantitative real-time polymerase chain reaction. Furthermore, typical vernalization unigenes VRN1 and VRN2 were identified, and also some vernalization-associated unigenes, such as CBF, SOC, TaAGL, AP2, LEA, LIM et al. were also annotated in the present study. As for VRN1 and VRN2, their expressions were consistent with some previous related studies. Also, this was the first time the vernalization genes VRN1 and VRN2 were founded in lily. According to the results of the present studies, we predicted that they would play an important role during vernalization in Lily Asiatic Hybrids; these data provided the foundation for the future studies of metabolism during vernalization of Asiatic lily.

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

“…During the annotation we identified novel isoforms for many potential orthologues of vernalization genes. A previous study measured expression of Asiatic lily bulbs before and after vernalization (27 days at 4 °C) using RNA-seq [ 33 ]. Both studies show that vernalization induces many cellular, biological and metabolic changes and similar genes, such as the SOC1 homologue, are found upregulated after cold treatment in the bulb meristem hinting that this gene, known to be involved in flowering, might play a role in the vernalization pathway.…”

“…A report about the transcriptome of Asiatic lily hybrid (cultivar Tiny Ghost) bulbs 27 days after exposure to 25 °C or 4 °C was recently published. The reported results revealed changes in the expression of a large number of genes belonging to several metabolic pathways and orthologs to vernalization genes in other plant species [ 33 ]. In that study, the length of cold exposure of the bulbs was established according to the peak in sugar content in the scales, however, the report does not specify the effect of cold exposure on flowering time, therefore, a definite association between the results and the actual vernalization process is not explicit.…”

Comparative Transcriptome Analysis of Gene Expression and Regulatory Characteristics Associated with Different Vernalization Periods in Brassica rapa

“…Studies on transcriptome regulation based on phenotypes is a powerful research method [29,30]. Using this analytical method, DEGs and related regulatory pathways produced by Asiatic lily and tropical lotus during vernalization have been investigated [31,32]. With regard to B. rapa, the reference genome has been updated for several generations, and various regulatory pathways have been continuously studied [33,34].…”

Biotechnological Advancements for Improving Floral Attributes in Ornamental Plants

“…RNA sequencing has been adopted to illustrate quantitative effects of bulb vernalization on flowering and facilitates gene expression in the meristems. Investigations involving lilly bulbs subjected to cold treatment revealed many feasible candidate genes involved in vernalization (Huang et al, 2014; Villacorta-Martin et al, 2015). …”