Phylogenetic and Functional Analysis of Miscanthus

Background Second-generation sequencing technologies ostensibly provide numerous means through which related species, lines/cultivars, and individuals can be rapidly and efficiently differentiated. The ability to distinguish between individuals at the molecular level is critical to those conducting animal/plant breeding, food safety/quality research, diagnostic and clinical testing, and evolutionary biology studies. Traditionally, classical genetic identification studies based on marker polymorphisms have been utilized, but such techniques are both time and labor intensive. Here, we describe the use of high-throughput cDNA sequencing coupled with SNP mapping as a rapid means of distinguishing between three closely related cultivars of the lignocellulosic bioenergy crop giant miscanthus (Miscanthus x giganteus), a plant of tremendous bioenergy importance. Results Computational analysis of rhizome-derived cDNA sequences demonstrates that the three Miscanthus x giganteus cultivars can be genetically differentiated from each other and from other Miscanthus species based on cDNA SNPs. Moreover, the resulting phylogenetic tree generated from SNP frequency data parallels the known breeding history of the cultivars and species examined. Our results show that some of the giant miscanthus samples exhibit considerable divergence at the RNA/DNA sequence level. We have utilized the sequence data generated in this research to construct the first publicly available draft of the Miscanthus exome and have functionally annotated the expressed genes using Gene Ontology methods. Conclusions Here we describe a method that utilizes high-throughput exome sequencing for differentiating between closely related genotypes of organisms without a reference genome, such as Miscanthus. We combine this sequence with functional annotations to set up preliminary resources that support functional modelling of Miscanthus data.