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.
Highlights
The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates
We report here high-depth sequencing of expressed mRNAs from a variety of M. × giganteus tissues as well as multiple accessions of M. sinensis and one accession of M. sacchariflorus
For M. × giganteus, RNASeq libraries were constructed from eleven organs at a variety of developmental stages and sequenced separately (Figure 1A)
Summary
The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. Miscanthus is a perennial C4 grass that belongs to the Andropogoneae tribe within the Poaceae family, which includes important agricultural crops for food and fuel such as sugarcane, sorghum, and maize. Following their introduction into the Western world in the 1930s [1], members of the Miscanthus genus are grown as ornamental crops in many regions of the United States due to their characteristically robust growth and attractive late-season inflorescence. Natural hybridization events between the two most predominant Miscanthus species, M. sinensis and M. sacchariflorus, have been reported [5,6].
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
