Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages

Abstract

Background: The vegetative growth is an important stage for plants when they conduct photosynthesis, accumulate and collect all resources needed and prepare for reproduction stage. Bamboo is one of the fastest growing plant species. The rapid growth of Phyllostachys edulis results from the expansion of intercalary meristem at the basal part of nodes, which are differentiated from the apical meristem of rhizome lateral buds. However, little is known about the major signaling pathways and players involved during this rapid development stage of bamboo. To study this question, we adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage.

Results: We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.

Conclusion: Significant changes occur in various signaling pathways during the development of rhizome lateral buds. It is crucial to understand how these changes are translated to Phyllostachys edulis fast growth. These results expand our knowledge on the Moso bamboo internodes fast growth and provide research basis for further study.

Keywords: Alternative splicing; DELLA protein; GA; Phyllostachys edulies; Phytohormone; RNA-Seq; Rhizome lateral bud.

Fig. 1

Phyllostachys edulis rhizome bud and shoot in different development stages. Stages of Phyllostachys edulis rhizome bud were characterized by the bud or shoot length. The samples collected for this study (MSAJ-01 ~ MSAJ-05) are germination stage (MSAJ-01), development stage 1 (MSAJ-02), development stage 2 (MSAJ-03), development stage 3 (MSAJ-04) and shoot stage (MSAJ-05)

Fig. 2

Transcriptome sequence reads analysis. a Sequencing Saturation Analysis. As more reads (x axis) were sequenced, the discovery of genes with more than 10 reads reached plateau. b and c Average reads coverage in gene relative position in germination stage (b) and in early shoot stage (c). The x axis represented relative position in gene sequence from start ‘0’ to end ‘1’. The y axis showed the average read coverage for each gene position. The genes are grouped according to the total reads coverage from 10 to 100%, as is shown on the right

Fig. 3

Summary of the features of novel genes. a and b Distribution of exon lengths (a) and intron lengths (b) for novel genes (brown) and previously annotated genes (green). c Distributions of genes in each functional category using Mapman. novel genes (green) and annotated genes (blue)

Fig. 4

Functional enrichment analysis of AS events and genetic variations discovered during transcriptome analysis. a Distrbution of Class I and Class II AS event in different domain families. Class I, blue; Class II, green. Red dot, enriched b and c Distribution of nonsynonymous mutation (b) and coding frameshift indels and premature termination codons (PTCs) (c) in protein domain family

Fig. 5

Activities of transcription factor families and axillary meristem development at germination and early shoot stage. a Distribution of putative transcription factors upregulated in germination (green) and early shoot (blue) stages. Red dot, the family is enriched in respective stage. b Differential expression of putative regulators in axillary meristem development. Green, significantly increased expression at germination stage; brown, significantly increased expression at early shoot stage

Fig. 6

Changes in putative carbohydrate metabolism pathway gene expressions in two development stage. Key players in EMP (a), TCA (b) and PPP (c) pathways were investigated for their expression in germination and early shoot stage. The G-fold number presented how the expression levels in germination compared to early shoot. Green, G-fold < − 2

Fig. 7

Changes in expression of putative IAA synthesis pathways genes. a Transcriptome analysis of putative genes related to auxin synthesis. Green, significantly increased expression at germination stage. b Relative expression of putative genes in (a) at various underground stages of rhizome bud development. Stage 1 ~ 5 are germination, development stage 1,2 and 3 and early shoot stage, respectively. For CYP79B2 and AMI1, only the first four stages were assayed due to sample availability. The expressions were measured by qPCR and results were normalized based on the germination stage (stage 1) data

Fig. 8

Changes in expression of putative BR signaling pathways genes. a Transcriptome analysis of putative genes related to BR synthesis. Red, significantly increased expression at early shoot stage. b Relative expression of putative genes in (a) at five underground stages of rhizome bud development. Stage 1,3,4 and 5 are germination, development stage 1 and 3, and early shoot stage, respectively. Top, BR signaling pathway derived from Kyoto Encyclopedia of Genes and Genomes Database. The expressions were measured by qPCR and results were normalized based on the germination stage (stage 1) data

Fig. 9

Changes in expression of putative GA signaling pathways genes. a Transcriptome analysis of putative genes related to GA signaling. Green, significantly increased expression at germination stage. Red, significantly increased expression at early shoot stage. B Relative expression of putative genes in (a) at five underground stages of rhizome bud development. Stage 1 ~ 5 are germination, development stage 1,2 and 3 and early shoot stage, respectively. Top, GA signaling pathway derived from Kyoto Encyclopedia of Genes and Genomes Database. The expressions were measured by qPCR and results were normalized based on the germination stage (stage 1) data

Fig. 10

GA stimulate the internode growth in Moso bamboo. a Treatment of water (left), PAC (middle) and GA (right) on Moso bamboo seedlings. b and c Distribution of internode lengths from basal (1) to apical (10) of seedlings. d Accumulation of PheDELLA was only detected in stem tissues of PAC treated seedlings. Red arrow, DELLA protein visualized in western blot. M, marker; L, leaves; S, stem. Bars, 3 cm