Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

Abstract

BackgroundMoso bamboo (Phyllostachys edulis) is a well-known bamboo species of high economic value in the textile industry due to its rapid growth. Phytohormones, which are master regulators of growth and development, serve as important endogenous signals. However, the mechanisms through which phytohormones regulate growth in moso bamboo remain unknown to date.ResultsHere, we reported that exogenous gibberellins (GA) applications resulted in a significantly increased internode length and lignin condensation. Transcriptome sequencing revealed that photosynthesis-related genes were enriched in the GA-repressed gene class, which was consistent with the decrease in leaf chlorophyll concentrations and the lower rate of photosynthesis following GA treatment. Exogenous GA applications on seedlings are relatively easy to perform, thus we used 4-week-old whole seedlings of bamboo for GA- treatment followed by high throughput sequencing. In this study, we identified 932 cis-nature antisense transcripts (cis-NATs), and 22,196 alternative splicing (AS) events in total. Among them, 42 cis-nature antisense transcripts (cis-NATs) and 442 AS events were differentially expressed upon exposure to exogenous GA3, suggesting that post-transcriptional regulation might be also involved in the GA3 response. Targets of differential expression of cis-NATs included genes involved in hormone receptor, photosynthesis and cell wall biogenesis. For example, LAC4 and its corresponding cis-NATs were GA3-induced, and may be involved in the accumulation of lignin, thus affecting cell wall composition.ConclusionsThis study provides novel insights illustrating how GA alters post-transcriptional regulation and will shed light on the underlying mechanism of growth modulated by GA in moso bamboo.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1336-z) contains supplementary material, which is available to authorized users.

Genome-wide analysis of GATA factors in moso bamboo (Phyllostachys edulis) unveils that PeGATAs regulate shoot rapid-growth and rhizome development

“…5b), we rationally hypothesized that the PeGATA genes are also tightly regulated by phytohormones. To test our hypothesis, we performed gene expression analysis of the PeGATA genes under GA and auxin treatment based on the RNA-seq data published in the previous studies [28, 40]. A total of 12 PeGATA genes showed significant gene expression under GA treatment (Fig.…”

“…It has been reported that several gene families are involved in flower development and abiotic stress [30–32, 41], the rapid-growth associated transcription factors remain elusive. The genome sequences of moso bamboo[33] and transcriptome studies [2, 27, 28, 40] provide important platforms for the identification of rapid-growth shoot and rhizome development associated gene families. The rapid-growth related genes could provide useful information for genetic manipulation of plant height in future.…”

“…To investigate gene expression levels of the PeGATA genes in different tissues or hormone treatments, RNA-seq data was downloaded from Short Read Archive (SRA) database for the lateral buds, rhizome tips and new shoot tips (SRP093919) [2], and bamboo seedlings under GA and auxin treatment (SRP119416 and SRP109631) [28, 40], respectively. The pair-end reads were mapped to the moso bamboo reference genome using tophat2, and differential expressed genes were detected by cufflinks with defaults parameters [52].…”

Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo (Phyllostachys edulis)

“…The first plant GATA factor was identified from Nicotiana tabacum [14]. GATA factors have been identified in many plant species, including Arabidopsis (29), rice (28), apple (35), and soybean (64) [9,10,15]. Plant GATA factors are involved in many developmental processes, affecting plant architecture [16], flower development [17], hypocotyl elongation [18], and seed germination [19].…”

“…Recently, large-scale transcriptome analysis has shown that light and phytohormones may play important roles in the rapid-growth of bamboo [27][28][29]. In addition, a large number of transcription factor families, involved in the abiotic stress response and flower development, have been studied in moso bamboo [30][31][32].…”