De novo transcriptome assembly for the tropical grass Panicum maximum Jacq

PLoS One. 2013 Jul 29;8(7):e70781. doi: 10.1371/journal.pone.0070781. Print 2013.

Abstract

Guinea grass (Panicum maximum Jacq.) is a tropical African grass often used to feed beef cattle, which is an important economic activity in Brazil. Brazil is the leader in global meat exportation because of its exclusively pasture-raised bovine herds. Guinea grass also has potential uses in bioenergy production due to its elevated biomass generation through the C4 photosynthesis pathway. We generated approximately 13 Gb of data from Illumina sequencing of P. maximum leaves. Four different genotypes were sequenced, and the combined reads were assembled de novo 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 cattle grazing and bioenergy production. The most abundant transcripts were involved in carbon fixation, photosynthesis, RNA translation and heavy metal cellular homeostasis. Finally, we identified a number of potential molecular markers, including 5,035 microsatellites (SSRs) and 346,456 single nucleotide polymorphisms (SNPs). To the best of our knowledge, this is the first study to characterize the complete leaf transcriptome of P. maximum using high-throughput sequencing. The biological information provided here will aid in gene expression studies and marker-assisted selection-based breeding research in tropical grasses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biomarkers
  • Brazil
  • Cattle
  • Computational Biology / methods
  • Gene Expression Profiling*
  • Gene Expression Regulation, Plant
  • High-Throughput Nucleotide Sequencing
  • Microsatellite Repeats
  • Molecular Sequence Annotation
  • Panicum / genetics*
  • Polymorphism, Single Nucleotide
  • Transcriptome*
  • Tropical Climate

Substances

  • Biomarkers

Grant support

The authors gratefully acknowledge the Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP) for financial support grant 2005/51010-0) and scholarships to GTS and CBCS, and the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for research fellowships to APS and LJ, and Embrapa Beef Cattle and Association for Promotion of Breeding Research in Tropical Forages (Unipasto) for financial support for field activities. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.