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      Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor

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          Abstract

          • Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular evolution of LTI pathway genes was important for Pooideae evolution.

          • Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize ( Zea mays), sorghum ( Sorghum bicolor), and rice ( Oryza sativa)) and five temperate Pooideae species ( Brachypodium distachyon, wheat ( Triticum aestivum), barley ( Hordeum vulgare), Lolium perenne and Festuca pratensis).

          • Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures of positive selection were significantly stronger in LTI trees after the rice and Pooideae split but before the Brachypodium divergence ( P < 0.05). Genome-wide heterogeneity in substitution rates was also observed, reflecting divergent genome evolution processes within these grasses.

          • Our results provide evidence for a link between adaptation to cold habitats and adaptive evolution of LTI stress responses in early Pooideae evolution and shed light on a poorly understood chapter in the evolutionary history of some of the world's most important temperate crops.

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          R: a language and environment for statistic computing

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            Evolutionary history of the grasses.

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              Unlocking the barley genome by chromosomal and comparative genomics.

              We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.
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                Author and article information

                Journal
                New Phytol
                New Phytol
                nph
                The New Phytologist
                Blackwell Publishing
                0028-646X
                1469-8137
                September 2013
                23 May 2013
                : 199
                : 4
                : 1060-1068
                Affiliations
                [1 ]Department of Medical Genetics, Oslo University Hospital and University of Oslo Oslo, Norway
                [2 ]Helmholtz Zentrum München, Institute of Bioinformatics and Systems Biology Ingolstädter Landstrasse 1, München, Germany
                [3 ]Department of Molecular Biology and Genetics, Aarhus University DK-4200, Slagelse, Denmark
                [4 ]Department of Plant and Environmental Sciences, Norwegian University of Life Sciences NO-1432, Ås, Norway
                Author notes
                Author for correspondence:, Simen Rød Sandve, Tel: +47 64965554, Email: simen.sandve@ 123456umb.no
                Article
                10.1111/nph.12337
                3840698
                23701123
                7d72ef23-8825-492a-ada4-d16e6fcfd579
                Copyright © 2013 New Phytologist Trust

                Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

                History
                : 19 March 2013
                : 18 April 2013
                Categories
                Research

                Plant science & Botany
                adaptive evolution,climate adaptation,cold,habitat shift,pooideae,temperate grasses

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