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Publication Type J
Authors Long, Y., J. W. Zhang, X. J. Tian, S. S. Wu, Q. Zhang, J. P. Zhang, Z. H. Dang and X. W. Pei
Title De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification
Source Bmc Genomics
Author Keywords Haloxylon ammodendron Drought Transcriptome Digital gene expression EST-SSR est-ssr markers hevea-brasiliensis reference genome soil-moisture cold stress transcriptome expression arabidopsis construction tolerance
Abstract Background: Haloxylon ammodendron (C. A. Mey.) is widely distributed across a range of habitats, including gravel desert, clay desert, fixed and semi-fixed sand, and saline land in Asian and African deserts. To date, no genomic information or expressed sequence tag-simple sequence repeat (EST-SSR) marker has been reported for H. ammodendron plants. Results: Using Illumina sequencing technology, we generated over two billion bases of high-quality sequence data on H. ammodendron and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 79,918 unigenes (mean length = 728 bp). Based on similarity searches comparing these unigenes with known proteins in the non-redundant (nr) protein database, 25,619 unigenes were functionally annotated with a cut-off E-value of 10(-5). In addition, DGE reads were mapped to the assembled transcriptome for gene expression analysis under drought stress. In total, 1,060 differentially expressed genes were identified. Among these genes, 356 genes were upregulated after drought treatment, and 704 genes were downregulated. We used the KEGG database to annotate these drought-induced genes; 207 unigenes were identified in the KEGG pathway annotation, and approximately 12.1% of the unigenes with known function fell into categories related to fatty acid metabolism, starch and sucrose metabolism, and nitrogen metabolism, suggesting that these pathways or processes may be involved in the drought response. Together, a total of 35 drought-inducible transcription factors were identified, including WRKY, MYB and bZIP family members. Conclusions: Our study is the first to provide a transcriptome sequence resource for H. ammodendron plants and to determine its digital gene expression profile under drought conditions using the assembled transcriptome data for reference. These data provide a valuable resource for genetic and genomic studies of desert plants under abiotic conditions.
Author Address [Long, Yan; Zhang, Jingwen; Tian, Xinjie; Wu, Shanshan; Pei, Xin Wu] Chinese Acad Agr Sci, Inst Biotechnol, Beijing 100081, Peoples R China. [Zhang, Qiong; Zhang, Jianping; Dang, Zhanhai] Gansu Agr Acad, Crop Inst, Lanzhou 730070, Peoples R China. Dang, ZH (reprint author), Gansu Agr Acad, Crop Inst, Lanzhou 730070, Peoples R China. 13669338239@163.com; peixinwu@caas.cn
ISSN 1471-2164
ISBN 1471-2164
29-Character Source Abbreviation BMC Genomics
Publication Date Dec
Year Published 2014
Volume 15
Digital Object Identifier (DOI) 10.1186/1471-2164-15-1111
Unique Article Identifier WOS:000346869400001
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