Transcriptome analysis of genes involved in secondary cell wall biosynthesis in developing internodes of Miscanthus lutarioriparius

Abstract

Miscanthus is a promising lignocellulosic bioenergy crop for bioethanol production. To identify candidate genes and regulation networks involved in secondary cell wall (SCW) development in Miscanthus, we performed de novo transcriptome analysis of a developing internode. According to the histological and in-situ histochemical analysis, an elongating internode of M. lutarioriparius can be divided into three distinct segments, the upper internode (UI), middle internode (MI) and basal internode (BI), each representing a different stage of SCW development. The transcriptome analysis generated approximately 300 million clean reads, which were de novo assembled into 79,705 unigenes. Nearly 65% of unigenes was annotated in seven public databases. Comparative profiling among the UI, MI and BI revealed four distinct clusters. Moreover, detailed expression profiling was analyzed for gene families and transcription factors (TFs) involved in SCW biosynthesis, assembly and modification. Based on the co-expression patterns, putative regulatory networks between TFs and SCW-associated genes were constructed. The work provided the first transcriptome analysis of SCW development in M. lutarioriparius. The results obtained provide novel insights into the biosynthesis and regulation of SCW in Miscanthus. In addition, the genes identified represent good candidates for further functional studies to unravel their roles in SCW biosynthesis and modification.

Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content

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Genome‐wide discovery of tissue‐specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

“…Remarkably, a substantial number of TFs with multiple connections to specific miRNAs and other genes involved in the biosynthesis of carbohydrates further implies that these subset of TF, miRNAs and genes might synergistically regulate the galactomannan biosynthesis. In addition, the presence of three common TFs such as NAC, MYB and bHLH, among the known and novel miRNA hub communities, further proves their synergetic role/or co‐expression during galactomannan synthesis (Hu et al ., ).…”

Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses

“…To achieve these goals, we first performed gene co-expression network analyses based on an extensive internode sampling scheme over three field trials. Indeed, the construction of co-expression networks has recently emerged as a powerful method to explore high throughput expression datasets and to dissect partially unknown physiological mechanisms (Higashi and Saito, 2013), including SCW establishment (Ruprecht et al, 2011;Hirano et al, 2013a;Hu et al, 2017;Sibout et al, 2017). We therefore updated the phylogenies of MYB and NAC TF families from nine different species to accurately describe the structures of these gene families FIGURE 6 | Focused representations of the cell wall transcription factors co-expression networks from the yellow (A) and pink (B) modules.…”