Abstract
HIGHLIGHT De novo transcriptome profiling of five tissues reveals candidate genes putatively involved in rhizome development in M. lutarioriparius.Miscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation bioethanol production. However, the genomic resource for this species is relatively limited thus hampers our understanding of the molecular mechanisms underlying many important biological processes. In this study, we performed the first de novo transcriptome analysis of five tissues (leaf, stem, root, lateral bud and rhizome bud) of M. lutarioriparius with an emphasis to identify putative genes involved in rhizome development. Approximately 66 gigabase (GB) paired-end clean reads were obtained and assembled into 169,064 unigenes with an average length of 759 bp. Among these unigenes, 103,899 (61.5%) were annotated in seven public protein databases. Differential gene expression profiling analysis revealed that 4,609, 3,188, 1,679, 1,218, and 1,077 genes were predominantly expressed in root, leaf, stem, lateral bud, and rhizome bud, respectively. Their expression patterns were further classified into 12 distinct clusters. Pathway enrichment analysis revealed that genes predominantly expressed in rhizome bud were mainly involved in primary metabolism and hormone signaling and transduction pathways. Noteworthy, 19 transcription factors (TFs) and 16 hormone signaling pathway-related genes were identified to be predominantly expressed in rhizome bud compared with the other tissues, suggesting putative roles in rhizome formation and development. In addition, a predictive regulatory network was constructed between four TFs and six auxin and abscisic acid (ABA) -related genes. Furthermore, the expression of 24 rhizome-specific genes was further validated by quantitative real-time RT-PCR (qRT-PCR) analysis. Taken together, this study provide a global portrait of gene expression across five different tissues and reveal preliminary insights into rhizome growth and development. The data presented will contribute to our understanding of the molecular mechanisms underlying rhizome development in M. lutarioriparius and remarkably enrich the genomic resources of Miscanthus.
Highlights
Global climate change and depleting fossil fuel reserves have spurred increased concerns in the pursuit of alternative renewable energy resources such as biofuels (Yuan et al, 2008)
Similar results were reported for M. × giganteus transcriptome, in which genes involved in “hormone signaling” pathways were significantly enriched in spring rhizomes, whereas genes associated with “amino acid metabolism and seed maturation” pathways were much higher represented in fall rhizomes (Barling et al, 2013)
A de novo assembly of transcriptome data from five tissues of M. lutarioriparius was performed with the main objective to provide preliminary insights into rhizome development
Summary
Global climate change and depleting fossil fuel reserves have spurred increased concerns in the pursuit of alternative renewable energy resources such as biofuels (Yuan et al, 2008). Miscanthus has been regarded as a promising bioenergy crop for lignocellulosic biofuel production due to its superior characteristics such as high biomass yield, perennial growth habitus, low water and fertilizer requirement, abiotic stress tolerance and broad adaptation to marginal land etc. The Miscanthus genus contains more than 14 species, most of which originate from southern and eastern Asia (Hodkinson et al, 2002). Among these species, Miscanthus lutarioriparius that is endemic to central China, is characterized by overwhelmingly higher biomass yield and outstanding restoration capability of marginal land compared with M. sacchariflorus and M. sinensis (Liu et al, 2012; Yan et al, 2012; Mi et al, 2014). M. lutarioriparius is currently the most widely cultivated species for biomass production in bioenergy and biorefinery in China (Mi et al, 2014)
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