Transcriptome Sequencing and Analysis of the Fast Growing Shoots of Moso Bamboo (Phyllostachys edulis)

Abstract

BackgroundThe moso bamboo, a large woody bamboo with the highest ecological, economic, and cultural value of all bamboos, has one of the highest growth speeds in the world. Genetic research into moso bamboo has been scarce, partly because of the lack of previous genomic resources. In the present study, for the first time, we performed de novo transcriptome sequencing and mapped to the moso bamboo genomic resources (reference genome and genes) to produce a comprehensive dataset for the fast growing shoots of moso bamboo.ResultsThe fast growing shoots mixed with six different heights and culms after leaf expansion of moso bamboo transcriptome were sequenced using the Illumina HiSeq™ 2000 sequencing platform, respectively. More than 80 million reads including 65,045,670 and 68,431,884 clean reads were produced in the two libraries. More than 81% of the reads were matched to the reference genome, and nearly 50% of the reads were matched to the reference genes. The genes with log 2 ratio > 2 or < −2 (P<0.001) were characterized as the most differentially expressed genes. 6,076 up-regulated and 4,613 down-regulated genes were classified into functional categories. Candidate genes which mainly involved transcript factors, plant hormones, cell cycle regulation, cell wall metabolism and cell morphogenesis genes were further analyzed and they may form a network that regulates the fast growth of moso bamboo shoots.ConclusionFirstly, our data provides the most comprehensive transcriptomic resource for moso bamboo to date. Candidate genes have been identified and they are potentially involved in the growth and development of moso bamboo. The results give a better insight into the mechanisms of moso bamboo shoots rapid growth and provide gene resources for improving plant growth.

Genome-Wide Transcriptional Profiling to Elucidate Key Candidates Involved in Bud Burst and Rattling Growth in a Subtropical Bamboo (Dendrocalamus hamiltonii)

“…Interestingly, a large number of metabolic pathways genes involved in growth were identified. Inclusion of rhizome under study resulted in significantly larger number of differentially expressed transcripts than reported earlier (Peng et al, 2013a). Maximum transcripts were found differentially expressed during T3 transition (GS to MS) suggesting highest physiological dissimilarities between growing and mature tissues.…”

“…Cell proliferation occurs in the specialized regions called meristems, a rich source of mitogenic components (such as phytohormones and carbohydrates) that regulate cell cycle progression. Role of transcription factors and hormones in meristem maintenance and cell expansion have been reported in many studies (Gutierrez, 2005; Hay and Tsiantis, 2005; Piazza et al, 2005; De Veylder et al, 2007; Wang et al, 2009; Rodriguez et al, 2010; Peng et al, 2013a). We found seven transcription factor families, namely GRAS (18 transcripts), NAC (11), WUSCHEL (1), KNOTTED-1-like homeobox (2), GRF (17), E2F (1), ARF (49), and WD (130) playing significant role in meristem maintenance.…”

“…Rhizome and shoot samples of cultivated Dh were collected (Figures 1D–H) in the forenoon during winter dormancy (December) and monsoon (August–October) based on previous inferences (Zhang et al, 1995; Peng et al, 2013a) to obtain comprehensive overview of genes involved in growth. Dormant rhizome (DR) samples were procured during winters (December) when the day length was 10 h: 20 min and temperature ~9°C.…”

“…Candidate genes ( Sucrose synthase, Cellulose synthase, BoSUT2, BoPAL1, Invertase ) associated with growth have been characterized in Bambusa oldhamii (tropical bamboo; Chiu et al, 2006; Hsieh et al, 2006, 2011; Chen et al, 2010; Gao et al, 2010). Past genome-wide efforts made to understand shoot growth were focused but limited to temperate bamboo ( P. edulis ) (Wang et al, 2009; He et al, 2013; Peng et al, 2013a,b). Moreover, India has 2nd richest bamboo bioresource after China, with ~130 species representing 18 genera (Kumar, 2004), spanning large area of temperate, subtropics and tropics.…”

Cloning and stress response analysis of the PeDREB2A and PeDREB1A genes in moso bamboo (Phyllostachys edulis)

“…The moso bamboo, Phyllostachys edulis (Carrière) J. Houzeau (synonym Phyllostachys heterocycla Carrière), is a large woody bamboo with the highest ecological, economic, and cultural value among all bamboos in Asia (Peng et al, 2013b). However, adverse environmental factors, especially drought, cold and salt stress, not only reduce the economic value of moso bamboo, but also limit its range.…”