Dataset Information

Shoot transcriptome of the giant reed, Arundo donax.

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 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. We envisage that these resources will promote and facilitate studies of the abiotic stress capabilities of this exotic plant species, which facilitates its invasive capacity.

SUBMITTER: Barrero RA

PROVIDER: S-EPMC4509983 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Shoot transcriptome of the giant reed, Arundo donax.

Barrero Roberto A RA Guerrero Felix D FD Moolhuijzen Paula P Goolsby John A JA Tidwell Jason J Bellgard Stanley E SE Bellgard Matthew I MI

Data in brief 20150122

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 ...[more]

PMID: 26217707

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Project description:BACKGROUND:Arundo donax has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited. RESULTS:We used RNA sequencing (RNA-Seq) to de novo assemble and characterize the A. donax leaf transcriptome. The sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an N50 of 1134 bp. TransDecoder and Trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to UniProtKB/Swiss-Prot and UniRef90 databases, searching for known transcripts, proteins, protein domains, and signal peptides. Furthermore, the unitranscripts were annotated by mapping them to the NCBI non-redundant, GO and KEGG pathway databases using Blast2GO. The transcriptome was also characterized by BLAST searches to investigate homologous transcripts of key genes involved in important metabolic pathways, such as lignin, cellulose, purine, and thiamine biosynthesis and carbon fixation. Moreover, a set of homologous transcripts of key genes involved in stomatal development and of genes coding for stress-associated proteins (SAPs) were identified. Additionally, 8364 simple sequence repeat (SSR) markers were identified and surveyed. SSRs appeared more abundant in non-coding regions (63.18%) than in coding regions (36.82%). This SSR dataset represents the first marker catalogue of A. donax. 53 SSRs (PolySSRs) were then predicted to be polymorphic between ecotype-specific assemblies, suggesting genetic variability in the studied ecotypes. CONCLUSIONS:This study provides the first publicly available leaf transcriptome for the A. donax bioenergy crop. The functional annotation and characterization of the transcriptome will be highly useful for providing insight into the molecular mechanisms underlying its extreme adaptability. The identification of homologous transcripts involved in key metabolic pathways offers a platform for directing future efforts in genetic improvement of this species. Finally, the identified SSRs will facilitate the harnessing of untapped genetic diversity. This transcriptome should be of value to ongoing functional genomics and genetic studies in this crop of paramount economic importance.

Project description:Salinization is one of the major causes of agricultural soil degradation worldwide. In arid and semi-arid regions with calcareous soils, phosphorus (P) deficiency further worsens the quality of salinized soils. Nonetheless, nutrient poor soils could be suitable of producing second-generation energy crops. Due to its high biomass production, Arundo donax L. (giant reed) is one of the most promising species for energy and second-generation biofuel production. A. donax can be propagated by micropropagation, an in vitro technique that produces high number of homogeneous plantlets. However, crop establishment is often compromised due to poor plantlet acclimatization to the soil environment. Arbuscular mycorrhizal fungi (AM) are components of soil-plant systems able to increase root phosphorus uptake and to confer the plant an increase tolerance to salinity with a consequent enhancement effect of plant growth and yield. In the present study, the relative importance of the early symbiosis establishment between AM fungi and A. donax micropropagated plantlets in the response to salt stress under low phosphorus availability was determined. A commercial inoculum which contained two different AM fungi species: Rhizophagus intraradices and Funneliformis mosseae was used. AM-symbionts (AM) and non-symbionts plants were grown at two phosphorus [2.5 ?M (C) and 0.5 mM (P)] and three NaCl (1, 75 and 150 mM) concentrations in a room chamber under controlled conditions. After 5 weeks, AM root colonization was 60, 26 and 15% in 1, 75 and 150 mM NaCl-treated plants, respectively. At 1 and 75 mM NaCl, AM plants showed increased growth. In all saline treatments, AM plants had decreased Na+ uptake, Na+ root-to-shoot translocation, Na+/K+ ratio and increased P and K use efficiencies with respect to C and P plants. AM improved the nutritional status of A. donax plants by enhancing nutrient use efficiency rather than nutrient uptake. Increased phosphorus use efficiency in AM plants could have benefited ion (Na+ and K+) uptake and/or allocation and ultimately ameliorate the plant's response to saline conditions.

Dataset Information

Shoot transcriptome of the giant reed, Arundo donax.

Publications

Shoot transcriptome of the giant reed, Arundo donax.

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