Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq
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ORIGINAL PAPER
Analysis of the barley leaf transcriptome under salinity stress using mRNA-Seq Mark Ziemann • Atul Kamboj • Runyararo M. Hove Shanon Loveridge • Assam El-Osta • Mrinal Bhave
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Received: 17 July 2012 / Revised: 23 January 2013 / Accepted: 29 January 2013 Ó Franciszek Go´rski Institute of Plant Physiology, Polish Academy of Sciences, Krako´w 2013
Abstract Salinity is a threat to crops in many parts of the world, and together with drought, it is predicted to be a serious constraint to food security. However, understanding the impact of this stressor on plants is a major challenge due to the involvement of numerous genes and regulatory pathways. While transcriptomic analyses of barley (Hordeum vulgare L.) under salt stress have been reported with microarrays, there are no reports as yet of the use of mRNA-Seq. We demonstrate the utility of mRNA-Seq by analysing cDNA libraries derived from acutely salt-stressed and unstressed leaf material of H. vulgare cv. Hindmarsh. The data yielded [50 million sequence tags which aligned to 26,944 sequences in the Unigene reference database. To gain maximum information, we performed de novo assembly of unaligned reads and discovered [3,800 contigs, termed novel tentative consensus sequences, which are either new, or significant improvements on current databases. Differential gene expression screening found 48 significantly up-regulated and 62 significantly down-regulated transcripts. The work provides comprehensive insights into genome-wide effects of salinity and is a new
Communicated by M. Stobiecki.
Electronic supplementary material The online version of this article (doi:10.1007/s11738-013-1230-0) contains supplementary material, which is available to authorized users. M. Ziemann S. Loveridge A. El-Osta Baker IDI Heart and Diabetes Institute, Melbourne, VIC 3004, Australia A. Kamboj R. M. Hove M. Bhave (&) Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Hawthorn, VIC 3122, Australia e-mail: [email protected]
resource for the study of gene regulation in barley and wheat. Further, the bioinformatics workflow may be applicable to other non-model plants to establish their transcriptomes and identify unique sequences. Keywords Salinity Barley Gene expression mRNA-Seq
Introduction Salt and drought stresses are the two most important environmental stresses which limit plant growth and development. Over 100 countries in the world have been identified to be affected by salinity, covering about 350 million hectares in 1989 (Rengasamy 2006), and the scale of the problem seems to be increasing at an alarming rate, with[800 M ha ([6 % of total land area) affected by 2000 (Munns and Tester 2008). Salinity, together with drought, has far-reaching implications for food security, economic sustainability and the irreplaceable biodiversity of any affected area, and the challenges are expected to be exacerbated by the projected impact of climate change. The effects of water-insufficiency
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