De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)

Abstract

BackgroundTranscriptome sequencing can be used to determine gene sequences and transcript abundance in non-model species, and the advent of next-generation sequencing (NGS) technologies has greatly decreased the cost and time required for this process. Transcriptome data are especially desirable in bamboo species, as certain members constitute an economically and culturally important group of mostly semelparous plants with remarkable flowering features, yet little bamboo genomic research has been performed. Here we present, for the first time, extensive sequence and transcript abundance data for the floral transcriptome of a key bamboo species, Dendrocalamus latiflorus, obtained using the Illumina GAII sequencing platform. Our further goal was to identify patterns of gene expression during bamboo flower development.ResultsApproximately 96 million sequencing reads were generated and assembled de novo, yielding 146,395 high quality unigenes with an average length of 461 bp. Of these, 80,418 were identified as putative homologs of annotated sequences in the public protein databases, of which 290 were associated with the floral transition and 47 were related to flower development. Digital abundance analysis identified 26,529 transcripts differentially enriched between two developmental stages, young flower buds and older developing flowers. Unigenes found at each stage were categorized according to their putative functional categories. These sequence and putative function data comprise a resource for future investigation of the floral transition and flower development in bamboo species.ConclusionsOur results present the first broad survey of a bamboo floral transcriptome. Although it will be necessary to validate the functions carried out by these genes, these results represent a starting point for future functional research on D. latiflorus and related species.

Investigating the MicroRNAomes of Two Developmental Phases of Dendrocalamus latiflorus (Poaceae: Bambusoideae) Inflorescences

“…miR156 and miR172, for example, regulate this phase change in several model plant species (Chen 2004;Yu et al 2010b). The grass family (Poaceae) has become a model system in comparative genomics, and the available grass genome sequences include Brachypodium distachyon, rice, maize, sorghum and foxtail millet (Peng et al 2010;Bennetzen et al 2012;Zhang et al 2012a;Vogel et al 2010;Schnable et al 2009;Paterson et al 2009;Goff et al 2002;Yu et al 2002). For most of these grasses, miRNAome studies have already been performed (Unver and Budak 2009;Zhang et al 2009;Bedell et al 2005;Reinhart et al 2002).…”

Global Transcriptome Analysis and Identification of the Flowering Regulatory Genes Expressed in Leaves of Lagerstroemia indica

“…By comparing the unigenes in the leaves of L. indica with the NCBI database, at least 115 unigenes were discovered that showed homology to known flowering related genes from other plants (Supplementary Table S1). The number of unigenes related to flowering time control in L. indica was slightly greater than the number in Poncirus trifoliate (Zhang et al, 2011), but was significantly lower than that in D. latiflorus (Zhang et al, 2012), which included a large amount of floral meristem identity genes. In this study, homologous genes in the four pathways related to flowering time control were more prevalent than in P. trifoliate and D. latiflorus (Zhang et al, 2011(Zhang et al, , 2012.…”

“…The number of unigenes related to flowering time control in L. indica was slightly greater than the number in Poncirus trifoliate (Zhang et al, 2011), but was significantly lower than that in D. latiflorus (Zhang et al, 2012), which included a large amount of floral meristem identity genes. In this study, homologous genes in the four pathways related to flowering time control were more prevalent than in P. trifoliate and D. latiflorus (Zhang et al, 2011(Zhang et al, , 2012. This result showed that the leaf transcriptome may be superior to the floral and floral bud transcriptomes on flowering time control.…”

“…Compared with the sequencing of expressed sequence tags, NGS techniques possess higher throughput, lower cost, and more rapid RNA sequencing. Zhang et al (2012) identified numerous putative sequences related to flowering time control and flower development in Dendrocalamus latiflorus by comparing its floral transcriptome to those of known plants, and 290 unigenes were discovered that were homologous to known flowering-related genes from other species. Zhang et al (2011) conducted a transcriptome profile analysis of the flowering molecular processes of a Poncirus trifoliata mutant and its wild-type counterpart using massively parallel signature sequencing, thereby identifying a large number of genes involved in early flowering development.…”

Transcriptome Characterization of the Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) and Expression Analysis of Candidate Phosphate Transporter Genes

“…In this study, a total of 236,529,278 clean reads and 35.47 Gbs of databases were obtained from Chinese fir transcriptomes, which is much more than any previously published transcriptome research on Chinese fir [23][24][25]43]. Due to a lack of homologous unigenes, the average length of unigenes for non-model plants is usually less than 500 bp [26,44,45]. Surprisingly, the unigenes we assembled revealed a mean length of 520 bp, which is longer than those achieved in previous studies of Chinese fir as reported by Huang et al [43].…”