title: A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  Illumina 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.
  
  
  CONCLUSIONS
  This 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.
authors: Adam
authors: A
authors: Barling
authors: Kankshita
authors: K
authors: Swaminathan
authors: Therese
authors: T
authors: Mitros
authors: Brandon T
authors: BT
authors: James
authors: Juliette
authors: J
authors: Morris
authors: Ornella
authors: O
authors: Ngamboma
authors: Megan C
authors: MC
authors: Hall
authors: Jessica
authors: J
authors: Kirkpatrick
authors: Magdy
authors: M
authors: Alabady
authors: Ashley K
authors: AK
authors: Spence
authors: Matthew E
authors: ME
authors: Hudson
authors: Daniel S
authors: DS
authors: Rokhsar
authors: Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois Urbana, 1206 West Gregory Drive, Urbana, IL 61801, USA. smoose@illinois.edu.
authors: Stephen P
authors: SP
authors: Moose
mesh_terms: D016000:Cluster Analysis; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059647:Gene-Environment Interaction; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D009928:Organ Specificity / Q000235:genetics; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D012060:Rejuvenation; D015203:Reproducibility of Results; D027343:Rhizome / Q000235:genetics*; D012621:Seasons; D059467:Transcriptome