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Authors Haiminen, N; Klaas, M; Zhou, ZY; Utro, F; Cormican, P; Didion, T; Jensen, CS; Mason, CE; Barth, S; Parida, L
Author Full Name Haiminen, Niina; Klaas, Manfred; Zhou, Zeyu; Utro, Filippo; Cormican, Paul; Didion, Thomas; Jensen, Christian Sig; Mason, Christopher E.; Barth, Susanne; Parida, Laxmi
Title Comparative exomics of Phalaris cultivars under salt stress
Source BMC GENOMICS
Language English
Document Type Article; Proceedings Paper
Conference Title 12th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics
Conference Date OCT 19-22, 2014
Conference Location Cold Spring Harbor Lab, Cold Spring Harbor, NY
Conference Host Cold Spring Harbor Lab
Keywords Plus DIFFERENTIAL EXPRESSION ANALYSIS; ALIGNMENT
Abstract Background: Reed canary grass (Phalaris arundinacea) is an economically important forage and bioenergy grass of the temperate regions of the world. Despite its economic importance, it is lacking in public genomic data. We explore comparative exomics of the grass cultivars in the context of response to salt exposure. The limited data set poses challenges to the computational pipeline. Methods: As a prerequisite for the comparative study, we generate the Phalaris reference transcriptome sequence, one of the first steps in addressing the issue of paucity of processed genomic data in this species. In addition, the differential expression (DE) and active-but-stable genes for salt stress conditions were analyzed by a novel method that was experimentally verified on human RNA-seq data. For the comparative exomics, we focus on the DE and stable genic regions, with respect to salt stress, of the genome. Results and conclusions: In our comparative study, we find that phylogeny of the DE and stable genic regions of the Phalaris cultivars are distinct. At the same time we find the phylogeny of the entire expressed reference transcriptome matches the phylogeny of only the stable genes. Thus the behavior of the different cultivars is distinguished by the salt stress response. This is also reflected in the genomic distinctions in the DE genic regions. These observations have important implications in the choice of cultivars, and their breeding, for bio-energy fuels. Further, we identified genes that are representative of DE under salt stress and could provide vital clues in our understanding of the stress handling mechanisms in general.
Author Address [Haiminen, Niina; Utro, Filippo; Parida, Laxmi] IBM TJ Watson Res, Computat Biol Ctr, Yorktown Hts, NY 10598 USA; [Klaas, Manfred; Barth, Susanne] Oak Pk Crops Res Ctr, Teagasc Crops Environm & Land Use Programme, Carlow, Ireland; [Zhou, Zeyu] IBM Res, Carlton, Vic 3053, Australia; [Cormican, Paul] Anim & Grassland Res & Innovat Ctr, Teagasc Anim & Biosci Res Dept, Dunsany, Meath, Ireland; [Didion, Thomas; Jensen, Christian Sig] DLF Trifolium, Div Res, Store Heddinge, Denmark; [Mason, Christopher E.] Weill Cornell Med Coll, New York, NY 10021 USA
Reprint Address Parida, L (corresponding author), IBM TJ Watson Res, Computat Biol Ctr, Yorktown Hts, NY 10598 USA.
E-mail Address parida@us.ibm.com
ResearcherID Number Haiminen, Niina/AAU-3068-2020; Barth, Susanne/P-3366-2014
ORCID Number Haiminen, Niina/0000-0002-8663-1019; Barth, Susanne/0000-0002-4104-5964; Utro, Filippo/0000-0003-3226-7642
Times Cited 5
Total Times Cited Count (WoS, BCI, and CSCD) 5
Publisher BMC
Publisher City LONDON
Publisher Address CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND
ISSN 1471-2164
29-Character Source Abbreviation BMC GENOMICS
ISO Source Abbreviation BMC Genomics
Publication Date OCT 17
Year Published 2014
Volume 15
Supplement 6
Article Number S18
Digital Object Identifier (DOI) 10.1186/1471-2164-15-S6-S18
Page Count 12
Web of Science Category Biotechnology & Applied Microbiology; Genetics & Heredity
Subject Category Biotechnology & Applied Microbiology; Genetics & Heredity
Document Delivery Number AU5ZY
Unique Article Identifier WOS:000345683000019
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