Transcriptome analysis of Miscanthus lutarioriparius

Miscanthus lutarioriparius is a promising lignocellulosic feedstock for second-generation biofuel production. However, the genomic resources 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, lateral bud, stem, root 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 public protein databases including NCBI non-redundant (NR) proteins, Protein family (Pfam), SwissProt, Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Differential gene expression profiling analysis revealed that 4,609, 3,188, 1,679, 1,218 and 1,077 genes were predominantly expressed in roots, leaves, stems, lateral buds, and rhizome buds, respectively. The expression patterns were classified into twelve distinct clusters. Pathway enrichment analysis revealed that genes predominantly expressed in rhizome buds were enriched in primary metabolism and hormone signaling and transduction pathways. Noteworthy, 19 transcription factors (TFs) and 16 hormone signaling pathway genes were identified to be predominantly expressed in rhizome buds compared with others, suggesting of putative roles in regulating rhizome formation and development. The predictive regulatory network was constructed between four TFs and six Auxin and Abscisic acid (ABA) -related genes. Furthermore, the expressions of 12 rhizome-specific genes were further validated by quantitative real-time RT-PCR (qRT-PCR) analysis. Taken together, this study provided a global portrait of gene expression patterns across different tissues and revealed deep 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.