de novo Assembly and Characterization of Leaf Transcriptome using Illumina Sequencing in Tropical Forage Panicum maximum

Panicum maximum Jacq. (Guinea grass) is a major forage grass in tropical and semitropical regions. Guinea grass is the most productive seed-propagated forage and the second most cultivated grass in Brazil, and also has potential uses in bioenergy production due to its elevated biomass generation through the C₄ photosynthesis pathway. Here, we sequenced Guinea grass leaves, resulting in approximately 13 Gb of data using Illumina GAIIx platform. Combined reads were de novo assembled into 38,192 unigenes and annotated; approximately 63% of the unigenes had homology to other proteins in the NCBI non-redundant protein database. Functional classification through COG (Clusters of Orthologous Groups), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses showed that the unigenes from Guinea grass leaves are involved in a wide range of biological processes and metabolic pathways, including C₄ photosynthesis and lignocellulose generation, which are important for livestock and bioenergy production. We also found 1,467 unigenes annotated as related to reproductive processes among GO terms, providing valuable information for further studies of Panicum-type apomixis mode of reproduction. Based on FPKM results, the most abundant transcripts were involved in carbon fixation, photosynthesis, RNA translation and heavy metal cellular homeostasis. Finally, we identified a number of putative molecular markers, including 5,035 microsatellites (SSRs) and 346,456 single nucleotide polymorphisms (SNPs). Orthology search against other grasses via reciprocal blast hit showed that phyletic relationships are conserved among transcripts. The biological information provided here will aid in gene expression studies and marker-assisted selection-based breeding research in tropical grasses.