干旱区生态环境知识资源中心(Arid): Shoot transcriptome of the giant reed, Arundo donax

Arid

DOI	10.1016/j.dib.2014.12.007
	Shoot transcriptome of the giant reed, Arundo donax
	Barrero, Roberto A.; Guerrero, Felix D.; Moolhuijzen, Paula; Goolsby, John A.; Tidwell, Jason; Bellgard, Stanley E.; Bellgard, Matthew I.
通讯作者	Bellgard, MI
来源期刊	DATA IN BRIEF
ISSN	2352-3409
出版年	2015
卷号	3 页码:1-6
英文摘要	The giant reed, Arundo donux, 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 Ilumina 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 Poaceac species. Of these 13,080 (47.58%), 6165 (2243%) 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. (C) 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license
英文关键词	Arundo donax Giant reed Shoot Transcriptome RNA de novo assembly RNA-Scq
类型	Article ; Data Paper
语种	英语
开放获取类型	DOAJ Gold, Green Published
收录类别	ESCI
WOS记录号	WOS:000453156300001
WOS类目	Multidisciplinary Sciences
WOS研究方向	Science & Technology - Other Topics
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/331477
作者单位	[Barrero, Roberto A.; Moolhuijzen, Paula; Bellgard, Matthew I.] Murdoch Univ, Ctr Comparat Genom, Murdoch, WA, Australia; [Guerrero, Felix D.] ARS, USDA, Knipling Bushland US Livestock Insects Res Lab, Kerrville, TX USA; [Goolsby, John A.; Tidwell, Jason] ARS, USDA, Cattle Fever Tick Res Lab, Edinburg, TX USA; [Bellgard, Stanley E.] Landcare Res Ltd, Auckland 1142, New Zealand
推荐引用方式 GB/T 7714	Barrero, Roberto A.,Guerrero, Felix D.,Moolhuijzen, Paula,et al. Shoot transcriptome of the giant reed, Arundo donax[J],2015,3:1-6.
APA	Barrero, Roberto A..,Guerrero, Felix D..,Moolhuijzen, Paula.,Goolsby, John A..,Tidwell, Jason.,...&Bellgard, Matthew I..(2015).Shoot transcriptome of the giant reed, Arundo donax.DATA IN BRIEF,3,1-6.
MLA	Barrero, Roberto A.,et al."Shoot transcriptome of the giant reed, Arundo donax".DATA IN BRIEF 3(2015):1-6.