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Data from: Shoot transcriptome of the giant reed, Arundo donax

dataset
posted on 2024-02-09, 18:21 authored by Roberto Barrero, Felix D. Guerrero, Paula M. Moolhuijzen, John A. Goolsby, Jason Tidwell, Stanley E. Bellgard, Matthew I. Bellgard

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 27,491 high confidence transcripts (≥200 bp) with at least 70% coverage of known genes in other Poaceae species. Of these 13,080 (47.58%), 6165 (22.43%) and 8246 (30.0%) transcripts have sequence similarity to known, domain-containing and conserved hypothetical proteins, respectively. We also report 75,590 low confidence transcripts supported by both trans-ABBySS and Velvet-Oases de novo assembly pipelines. Within the low confidence subset of transcripts we identified partial hits to known (19,021; 25.16%), domain-containing (7093; 9.38%) and conserved hypothetical (16,647; 22.02%) proteins. Additionally 32,829 (43.43%) transcripts encode putative hypothetical proteins unique to A. donax. Functional annotation resulted in 5,550 and 6,070 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. It is envisaged that these resources will promote and facilitate studies of the abiotic stress capabilities of this exotic plant species, which facilitates its invasive capacity. Supplemental Excel data files with the article detail functional annotation of Arundo donax high confidence and low confidence genes. Data are also available at https://www.ncbi.nlm.nih.gov/nuccore/GBRH01000000 . The assembled and annotated A. donax USA genotype Rio Grande RNA transcriptome has been deposited at DDBJ/EMBL/GenBank under the project accession PRJNA256910.


Resources in this dataset:

  • Resource Title: Shoot transcriptome of the giant reed, Arundo donax.

    File Name: Web Page, url: https://www.sciencedirect.com/science/article/pii/S2352340914000377

    *Data in Brief* article reporting the assembly of 27,491 high confidence transcripts (≥200 bp) for the giant reed, *Arundo donax* with at least 70% coverage of known genes in other Poaceae species.

Funding

USDA-ARS: 6205-32000-031-00

History

Data contact name

Bellgard, Matthew I.

Publisher

Data in Brief

Intended use

It is envisaged that these resources will promote and facilitate studies of the abiotic stress capabilities of this exotic plant species, which facilitates its invasive capacity. First transcriptome sequence data made available in GenBank/DDBJ/Embbl for the A. donax invasive Rio Grande basin genotype. The A. donax shoot transcriptome dataset provides insights into one of the fastest growing terrestrial plants. A. donax has high tolerance to abiotic stresses and its high invasive nature threatens many natural environments and ecosystems. The abundant biomass of A. donax plants makes it an ideal candidate for biofuel programs.

Theme

  • Not specified

Geographic location - description

Laredo, Texas, United States; Rio Grande River

ISO Topic Category

  • biota
  • environment
  • inlandWaters

National Agricultural Library Thesaurus terms

Arundo donax; perennials; grasses; invasive species; plants (botany); water resources; biological control agents; environmental factors; water stress; heavy metals; salinity; data collection; standard operating procedures; transcriptome; shoots; genotype; Rio Grande River; Texas; Mexico; genes; Poaceae; sequence homology; pipelines; gene ontology; spliceosomes; ribosomes; ubiquitin; proteolysis; RNA; oxidative phosphorylation; biochemical pathways; heat stress; introduced plants; abiotic stress; biofuels

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Barrero, Roberto; Guerrero, Felix D.; Moolhuijzen, Paula M.; Goolsby, John A.; Tidwell, Jason; Bellgard, Stanley E.; Bellgard, Matthew I. (2018). Data from: Shoot transcriptome of the giant reed, Arundo donax. Data in Brief. https://doi.org/10.1016/j.dib.2014.12.007

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