Comparative exomics of Phalariscultivars under salt stress

BMC Genomics

Research

Laxmi Parida¹  Niina Haiminen¹  Filippo Utro¹  Christian Sig Jensen²  Thomas Didion²  Zeyu Zhou³  Paul Cormican⁴  Manfred Klaas⁵  Susanne Barth⁵  Christopher E Mason⁶ 

[1] Computational Biology Center, IBM T. J. Watson Research, 10598, Yorktown Heights, NY, USA;DLF-Trifolium, Research Division, Store Heddinge, Denmark;IBM Research, 3053, Carlton, VIC, Australia;Teagasc Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland;Teagasc Crops Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland;Weill Cornell Medical College, 10021, New York, NY, USA;

关键词: Differential Expression;    RNA-sequencing;    Salt stress;    Transcriptomics;    Phalaris;    Reed canary grass;    Human brain data;    Stable genes;    Non-parametric model;   

DOI  :  10.1186/1471-2164-15-S6-S18

来源: Springer

【 摘 要 】

BackgroundReed 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.MethodsAs 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 conclusionsIn 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.

【 授权许可】

Unknown   
© Haiminen et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.