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

Jian Gao,Zhenhua Peng,Chunling Zhang,Feiyan Qi,Shaohua Mu,Ying Zhang,Xueping Li,Emmanuel Gaquerel

doi:10.1371/journal.pone.0098910

Abstract

BackgroundAs 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.ResultsWe 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.ConclusionWe 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.

Highlights

Transcriptome sequencing is a convenient way of rapidly obtaining information on the expressed fraction of a genome [1]
Sequence data quality control and filtering In order to get an overview of the Moso bamboo transcriptome, we generated cDNA libraries from leaves of non-flowering plants and mixed RNA extracted from panicles at four different flowering developmental stages using paired-end sequencing by the Illumina platform
The reads mapping to the reference genome dataset To identify the genes corresponding to these clean reads in each library, the clean reads were mapped to the reference genes expressed in the Moso bamboo genome

Summary

Introduction

Transcriptome sequencing is a convenient way of rapidly obtaining information on the expressed fraction of a genome [1]. Next-generation sequencing (NGS) technology, such as the Illumina Solexa, Roche 454 and ABI SOLiD platforms, has emerged as a cost-effective approach for high-throughput sequencing. It has revolutionized biological research by rapidly providing genomic and transcriptomic data [2,3,4]. RNA-Seq analysis is powerful, enabling large-scale functional assignments of genes via the assembly of large sequenced transcriptome library. With this technique, quantitative analysis of gene expression can be performed without potential bias, allowing a more sensitive and accurate profiling of the transcriptome [7,8]. 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

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