Shoot transcriptome of the Giant Reed, Arundo donax

Authors: BARRERO, ROBERTO - Murdoch University; Guerrero, Felicito; MOOLHUIJZEN, PAULA - Murdoch University; Goolsby, John; BELLGARD, STANLEY - Landcare Research; Tidwell, Jason; BELLGARD, MATTHEW - Murdoch University

Submitted to: Genomics Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2015
Publication Date: 1/22/2015
Publication URL: https://handle.nal.usda.gov/10113/62126
Citation: Barrero, R., Guerrero, F., Moolhuijzen, P., Goolsby, J., Bellgard, S., Tidwell, J.P., Bellgard, M. 2015. Shoot transcriptome of the Giant Reed, Arundo donax. Genomics Data. 3:1-6.

Interpretive Summary: The giant reed, Arundo donax, is a perennial grass species that has become an invasive plant in many countries, including the United States. This plant grows under adverse environmental conditions, displaying insensitivity to drought stress, flooding, heavy metals, salinity and competition from other plants, making control very difficult. Huge stands of A. donax have significant negative impacts on available water resources and efforts are underway to identify biological control agents against this species. Knowledge about the genetics of this species is important to help develop novel control technologies. To establish a gene-based dataset, we used next-generation sequencing to identify gene expression in actively growing shoots from an invasive genotype collected along the Rio Grande River in Texas. We report the assembly of this dataset consisting of 293,411 sequences from expressed genes. We found only 34.15% of these sequences had similarity to known proteins. We also found 12, 9, and 4 sequences with functions noted as stress-related, heat stress, and water stress proteins, respectively. We envisage that this sequence resource will facilitate a robust study of the stress responses of this plant species at the genetic level with the aim of determining the genetic source of its invasiveness.

Technical Abstract: The giant reed, Arundo donax, is a perennial grass species that has become an invasive plant in many countries. Expansive stands of A. donax have significant negative impacts on available water resources and efforts are underway to identify biological control agents against this species. The giant reed grows under adverse environmental conditions, displaying insensitivity to drought stress, flooding, heavy metals, salinity and herbaceous competition, thus hampering control programs. To establish a foundational molecular dataset, we used an llumina Hi-Seq protocol to sequence the transcriptome of actively growing shoots from an invasive genotype collected along the Rio Grande River, bordering Texas and Mexico. We report the assembly of 293,411 transcripts (>=200bp) encoding 170Mbp. We found 100,212 (34.15%) and 65,532 (22.33%) transcripts with sequence similarity to known and hypothetical proteins, respectively. Functional annotation resulted in 44,933 and 15,071 transcripts with assigned Gene Ontology and KEGG pathway information, respectively. The most abundant KEGG pathways are spliceosome, ribosome, ubiquitin mediated proteolysis, plant-pathogen interaction, RNA degradation and oxidative phosphorylation metabolic pathway. Furthermore, we also found 12, 9, and 4 transcripts annotated as stress-related, heat stress, and water stress proteins, respectively. We envisage that these resources will promote and facilitate a robust study of the abiotic stress capabilities of this exotic plant species, which facilitates its invasive capacity.