A detailed gene expression study of the Miscanthusgenus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes

Abstract

BackgroundThe Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and future genetic improvement. A comprehensive catalog of expressed sequences were generated from a variety of Miscanthus species and tissue types, with an emphasis on characterizing gene expression changes in spring compared to fall rhizomes.ResultsIllumina short read sequencing technology was used to produce transcriptome sequences from different tissues and organs during distinct developmental stages for multiple Miscanthus species, including Miscanthus sinensis, Miscanthus sacchariflorus, and their interspecific hybrid Miscanthus × giganteus. More than fifty billion base-pairs of Miscanthus transcript sequence were produced. Overall, 26,230 Sorghum gene models (i.e., ~ 96% of predicted Sorghum genes) had at least five Miscanthus reads mapped to them, suggesting that a large portion of the Miscanthus transcriptome is represented in this dataset. The Miscanthus × giganteus data was used to identify genes preferentially expressed in a single tissue, such as the spring rhizome, using Sorghum bicolor as a reference. Quantitative real-time PCR was used to verify examples of preferential expression predicted via RNA-Seq. Contiguous consensus transcript sequences were assembled for each species and annotated using InterProScan. Sequences from the assembled transcriptome were used to amplify genomic segments from a doubled haploid Miscanthus sinensis and from Miscanthus × giganteus to further disentangle the allelic and paralogous variations in genes.ConclusionsThis large expressed sequence tag collection creates a valuable resource for the study of Miscanthus biology by providing detailed gene sequence information and tissue preferred expression patterns. We have successfully generated a database of transcriptome assemblies and demonstrated its use in the study of genes of interest. Analysis of gene expression profiles revealed biological pathways that exhibit altered regulation in spring compared to fall rhizomes, which are consistent with their different physiological functions. The expression profiles of the subterranean rhizome provides a better understanding of the biological activities of the underground stem structures that are essentials for perenniality and the storage or remobilization of carbon and nutrient resources.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-864) contains supplementary material, which is available to authorized users.

De novo transcriptome assembly of sugarcane leaves submitted to prolonged water-deficit stress

“…For annotation of the transcripts, we used other reference databases: the transcriptomes and proteomes predicted for Arabidopsis thaliana and Sorghum bicolor, both obtained from the repository of the Phytozome platform (v.10) (Goodstein et al, 2012), the available sugarcane transcriptomes SoGI (v.3.0) (Saccharum officinarum Gene Index) and SCG (SugarCane Genes) (v.1.0) (Grativol et al, 2014), ESTs of the dbEST database (Boguski et al, 1993), GenBank mRNAs for Saccharum spp., UniGene of Saccharum officinarum, and available data of Miscanthus giganteus (Barling et al, 2013). The analyses consisted of a comparison of the assembly with reference transcriptomes at the nucleotide (BLASTn) and amino acid level (BLASTx/tBLASTx), and with proteomes only at the amino acid level (BLASTx/tBLASTn).…”

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae)

“…After eliminating those primers that failed to amplify products from all taxa, 50 primer pairs in total were used (Table S1). Of these primers, 22 pairs amplified two genomic copies of the RNA contig, implying that the existence of paralogs is likely due to recent genome duplication in Miscanthus Swaminathan et al, 2012;Barling et al, 2013). It is known that incorporating paralogous sequences into phylogenetic analysis often leads to erroneous inferences of species phylogeny.…”

Distinct and overlapping functions ofMiscanthus sinensisMYB transcription factors SCM1 and MYB103 in lignin biosynthesis

“…Moreover, Miscanthus breeding has focused on the development of molecular markers to facilitate selection of varieties with improved biomass yield and/or composition (da Costa et al ., 2017). Genetic resources for Miscanthus, such as an extensive transcriptome database (Barling et al ., 2013) and a recently completed Miscanthus sinensis draft genome ( Miscanthus sinensis v7.1 DOE-JGI, http://phytozome.jgi.doe.gov/), are now available to explore biological processes with molecular approaches. A detailed, mechanistic understanding of SCW formation has the potential to complement marker-assisted breeding of novel Miscanthus traits with tailored biomass.…”