Characterization of the floral transcriptome of Moso bamboo (Phyllostachys edulis) at different flowering developmental stages by transcriptome sequencing and RNA-seq analysis

Abstract

Background: As an arborescent and perennial plant, Moso bamboo (Phyllostachys edulis (Carrière) J. Houzeau, synonym Phyllostachys heterocycla Carrière) is characterized by its infrequent sexual reproduction with flowering intervals ranging from several to more than a hundred years. However, little bamboo genomic research has been conducted on this due to a variety of reasons. Here, for the first time, we investigated the transcriptome of developing flowers in Moso bamboo by using high-throughput Illumina GAII sequencing and mapping short reads to the Moso bamboo genome and reference genes. We performed RNA-seq analysis on four important stages of flower development, and obtained extensive gene and transcript abundance data for the floral transcriptome of this key bamboo species.

Results: We constructed a cDNA library using equal amounts of RNA from Moso bamboo leaf samples from non-flowering plants (CK) and mixed flower samples (F) of four flower development stages. We generated more than 67 million reads from each of the CK and F samples. About 70% of the reads could be uniquely mapped to the Moso bamboo genome and the reference genes. Genes detected at each stage were categorized to putative functional categories based on their expression patterns. The analysis of RNA-seq data of bamboo flowering tissues at different developmental stages reveals key gene expression properties during the flower development of bamboo.

Conclusion: We showed that a combination of transcriptome sequencing and RNA-seq analysis was a powerful approach to identifying candidate genes related to floral transition and flower development in bamboo species. The results give a better insight into the mechanisms of Moso bamboo flowering and ageing. This transcriptomic data also provides an important gene resource for improving breeding for Moso bamboo.

Figure 1. Changes in gene expression profile among the different flower developmental stages.

The number of up-regulated and down-regulated genes between CK and F1; CK and F2; CK and F3; CK and F4; F1 and F2; F1 and F3; F1 and F4; F2 and F3; F2 and F4; F3 and F4 are summarized. DEGs: Differentially Expressed Genes.

Figure 2. Clustering of genes involved in bamboo flowering expression profiles at four different flower developmental stages.

Figure 3. The expression profiles of 8 selected genes from flowering tissues in different flower developmental stages and leaves of non-flowering of Moso bamboo.

The transcript levels were normalized to that of TIP41 (tonoplast intrinsic protein 41), and the level of each gene in the control was set at 1.0. Error bars represent the SD for three independent experiments. CO (CONSTANS), GID1 (gibberellin receptor GID1), DOF (Dof zinc finger protein 12), MYB (MYB transcription factor), FIP3 (phytochrome- interacting factor 3), MADS-14 (MADS-box gene-14), MADS-15 (MADS-box gene-15), LHY (late elongated hypocotyl).

Figure 4. A hypothesized pathways in regulation of flowering in Moso bamboo.

Yellow and red oval indicate that the involved genes are more highly expressed in the floral tissues, whereas blue oval indicate that the genes are down-expressed and green oval indicate that the genes are not activated. Purple dashed arrows represent pathways that were not used during flowering. Black arrow represents promotion. Green bar represents suppression.

Figure 5. Examples of sampled floral tissues.

A1-A2: Representatives of flowers collected to produce the sample for F1 (floral bud formation stage). B1-B2: Representatives of flowers collected to produce the sample for F2 (inflorescence growing stage). C1-C2: Representatives of flowers collected to produce the sample for F3 (bloom stage, flowers with both pistils and stamens emerging from glumes). D1-D3: Representatives of flowers collected to produce the sample for F4 (embryo formation stage).