RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation

Abstract

BackgroundFloral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an inflorescence have not been reported. We analyzed gene expression during Arabidopsis thaliana meristem development under long day conditions from day 7 to 16 after germination in one-day increments.ResultsThe dynamics of the expression of the main flowering regulators was consistent with previous reports: notably, the expression of FLOWERING LOCUS C (FLC) decreased over the course of the time series while expression of LEAFY (LFY) increased. This analysis revealed a developmental time point between 10 and 12 days after germination where FLC expression had decreased but LFY expression had not yet increased, which was characterized by a peak in the number of differentially expressed genes. Gene Ontology (GO) enrichment analysis of these genes identified an overrepresentation of genes related to the cell cycle.ConclusionsWe discovered an unprecedented burst of differential expression of cell cycle related genes at one particular point during transition to flowering. We suggest that acceleration of rate of the divisions and partial cell cycling synchronization takes place at this point.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1688-9) contains supplementary material, which is available to authorized users.

An RNA-Seq Bioinformatics Pipeline for Data Processing of Arabidopsis Thaliana Datasets

“…Consistent with the experimental findings, our results 475 as shown in Fig. 8 (a, b, c and d) displays higher mean PCC of 0.86 and 0.88 for FLC and LFY, 476 respectively which is consistent with published results (Michaels, 1999;Klepikova et al, 2015). 477…”

“…Using PCC metric, we evaluated similarity 473 in expression profiles of FLC and LFY obtained in this study and compared with profiles obtained 474 from Klepikova et al (Klepikova et al, 2015). Consistent with the experimental findings, our results 475 as shown in Fig.…”

“…Experiments were conducted by Klepikova et al (Klepikova et al, 2015) where a single A. thaliana 104 plant (Col-0) was grown in conditions for preventing crossbreeding. Plants were harvested at 7-105 16 days old to obtain synchronized plants at different developmental stages, denoted by S7 to 106 S16 respectively.…”

“…Analysis of A. thaliana apical shoot data suggest that certain known genes are 28 commonly regulated during the transition phase (Klepikova et al, 2015). Recent RNA-Seq studies 29…”

“…and Hochberg approach (Benjamini and Hochberg, 1995 An apical shoot meristem time-series dataset has been deposited by other researchers in the 234 NCNI SRA database under project ID PRJNA268115 (Klepikova et al, 2015) has been used in 235 this study. Analysis pipelines listing the data processing and differential gene expression steps 236 constructed and revealed through our research has been provided as Linux shell scripts which 237 can downloaded from GitHub https://github.com/deshpan4/RNA-Seq-pipeline.…”