| 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 |
