Towards uncovering the roles of switchgrass peroxidases in plant processes

Abstract

Herbaceous perennial plants selected as potential biofuel feedstocks had been understudied at the genomic and functional genomic levels. Recent investments, primarily by the U.S. Department of Energy, have led to the development of a number of molecular resources for bioenergy grasses, such as the partially annotated genome for switchgrass (Panicum virgatum L.), and some related diploid species. In its current version, the switchgrass genome contains 65,878 gene models arising from the A and B genomes of this tetraploid grass. The availability of these gene sequences provides a framework to exploit transcriptomic data obtained from next-generation sequencing platforms to address questions of biological importance. One such question pertains to discovery of genes and proteins important for biotic and abiotic stress responses, and how these components might affect biomass quality and stress response in plants engineered for a specific end purpose. It can be expected that production of switchgrass on marginal lands will expose plants to diverse stresses, including herbivory by insects. Class III plant peroxidases have been implicated in many developmental responses such as lignification and in the adaptive responses of plants to insect feeding. Here, we have analyzed the class III peroxidases encoded by the switchgrass genome, and have mined available transcriptomic datasets to develop a first understanding of the expression profiles of the class III peroxidases in different plant tissues. Lastly, we have identified switchgrass peroxidases that appear to be orthologs of enzymes shown to play key roles in lignification and plant defense responses to hemipterans.

Keywords: Hemiptera; ROS; biotic stress; lignin; peroxidases; switchgrass.

FIGURE 1

Phylogenetic clustering of heme- and thiol peroxidases (Prx) present in the switchgrass genome. Heme peroxidases (oval) consist of the class I ascorbate peroxidases (green), and class III peroxidases (red). Thiol peroxidases (circle) consist of the glutathione peroxidases (purple), peroxiredoxin (blue) and glutaredoxin (cyan).

FIGURE 2

Phylogenetic relationships and numbers within each evolutionary clade, as defined for rice, for switchgrass class III peroxidases. The distribution of peroxidases relative to the out-group sequences (blue lines) are shown in the circular phylogram. The rice and ancient peroxidase protein sequences used as representatives for these analyses, and the numbers of switchgrass members in each clade are indicated. The peroxidase sequences include loci from both the A and B genomes.

FIGURE 3

One-way clustering color map for class III peroxidase expression profiles (z-scores) for publically available NGS datasets for cultivars Summer and Alamo. Stages of plant development are early vegetative (EV), stem elongation (SE), and reproductive (RP) are as described in these datasets. Roots = Rt; Shoot = Sh; Flowers = Fwr. Red indicates high abundance, yellow is intermediate and green and blue are low or negligible abundance. The appropriate SRA identification numbers for these individual NGS files are shown inTable A1 in Appendix.

FIGURE 4

for crowns and rhizomes obtained from field-grown Summer plants at the Agricultural Research and Development Center fields of the University of Nebraska. Harvest months are shown and coincided approximately with green-up (May), late vegetative stage (June), flowering (July), hard-seed stage (Aug), and aerial senescence after a killing frost (Oct). Red indicates high abundance, yellow is intermediate and green and blue are low or negligible abundance. The appropriate SRA identification numbers for these individual NGS files are shown inTable A1 in Appendix. The six clusters of the most abundant transcripts from each harvest date are shown (C1–C6) along with the numbers of individual peroxidases as assigned to an evolutionary group.