Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes.

Cristiane P G Calixto,Robbie Waugh,John W S Brown

doi:10.1007/s00239-015-9665-0

Cristiane P G Calixto, Robbie Waugh + Show 1 more

Open Access

https://doi.org/10.1007/s00239-015-9665-0

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Abstract

The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to plant performance and productivity and to the adaptation and geographical range over which crops can be grown. To understand the clock in barley and how it relates to the components in the Arabidopsis thaliana clock, we have performed a systematic analysis of core circadian clock and clock-associated genes in barley, Arabidopsis and another eight species including tomato, potato, a range of monocotyledonous species and the moss, Physcomitrella patens. We have identified orthologues and paralogues of Arabidopsis genes which are conserved in all species, monocot/dicot differences, species-specific differences and variation in gene copy number (e.g. gene duplications among the various species). We propose that the common ancestor of barley and Arabidopsis had two-thirds of the key clock components identified in Arabidopsis prior to the separation of the monocot/dicot groups. After this separation, multiple independent gene duplication events took place in both monocot and dicot ancestors.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-015-9665-0) contains supplementary material, which is available to authorized users.

Highlights

Most living organisms optimise their day/night responses by measuring time and using this information to organize their physiology and morphology in anticipation of daily changes (Chen and McKnight 2007; Green et al 2002; Okamura 2004)
To understand the clock in barley and how it relates to the components in the Arabidopsis thaliana clock, we have performed a systematic analysis of core circadian clock and clock-associated genes in barley, Arabidopsis and another eight species including tomato, potato, a range of monocotyledonous species and the moss, Physcomitrella patens
We have identified orthologues and paralogues of Arabidopsis genes which are conserved in all species, monocot/dicot differences, species-specific differences and variation in gene copy number

Summary

Introduction

Most living organisms optimise their day/night responses by measuring time and using this information to organize their physiology and morphology in anticipation of daily changes (Chen and McKnight 2007; Green et al 2002; Okamura 2004). A relatively small number of genes establish and maintain the circadian rhythm of the clock. These core clock components are present in each cell and consist of a complex network of genes regulated by transcriptional feedback loops, post-transcriptional and post-translational modifications (Gallego and Virshup 2007; James et al 2012; McClung 2014; Sanchez et al 2010; Troein et al 2009) (Fig. 1). The framework of the Arabidopsis circadian clock known as the interlocking-loop model comprises at least three interlocking gene expression feedback loops (Harmer 2010; Locke et al 2006; Pokhilko et al 2010; Zeilinger et al 2006)

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