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(American Journal of Botany. 2009;96:1319-1336.) doi: 10.3732/ajb.0800340 © 2009 Botanical Society of America, Inc.

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Phytochrome gene expression and phylogenetic analysis in the short-day plant Pharbitis nil (Convolvulaceae): Differential regulation by light and an endogenous clock¹

² Section of Plant Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, California 95616 USA ³ Department of Plant Sciences, Center for Plant Diversity, UC Davis Herbarium, College of Agriculture and Environmental Sciences, 2041 Wickson Hall, University of California, Davis USA

ABSTRACT

To investigate the role of distinct phytochrome pools in photoperiodic timekeeping, we characterized four phytochrome genes in the short-day plant Pharbitis nil. Each PHY gene had different photosensory properties and sensitivity to night break that inhibits flowering. During extended dark periods, PHYE, PHYB, and PHYC mRNA accumulation exhibited a circadian rhythmicity indicative of control by an endogenous clock. Phylogenetic analysis recovered four clades of angiosperm phytochrome genes, phyA, phyB, phyC, and phyE. All except the phyE clade included sequences from both monocots and eudicots. In addition, phyA is sister to phyC and phyE sister to phyB, with gymnosperm sequences sister to either the phyA-phyC clade or to the phyB-phyE clade. These results suggest that a single duplication occurred in an ancestral seed plant before the divergence of extant gymnosperms from angiosperms and that two subsequent duplications occurred in an ancestral angiosperm before the divergence of monocots from eudicots. Thus in P. nil, a multigene family with different patterns of mRNA abundance in light and darkness contributes to the total phytochrome pool: one pool is light labile (phyA), whereas the other is light stable (phyB and phyE). In addition, PHYC mRNA represents a third phytochrome pool with intermediate photosensory properties.

Key Words: circadian rhythm • Convolvulaceae • endogenous clock • flowering • night break • Pharbitis nil • photoperiodism • phylogeny • phytochrome • short-day plant

Received for publication 7 October 2008. Accepted for publication 11 February 2009.

FOOTNOTES

¹ The authors are thankful for the Professor Grady Webster Memorial Fund and its generous support of this research. The authors thank Professor Abraham H. Halevy (Hebrew University of Jerusalem, Israel) and Dr. A. Kadman-Zahavi (ARO, Volcani Center, Israel) for stimulating discussions about Pharbitis nil and photoperiodic floral induction. They also thank the two anonymous reviewers for helpful comments that improved this article. This research was supported by National Science Foundation Grant No. IOB 97-17249 (Developmental Systems) to S.O’N.

⁴ Present address: College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 PR China

⁵ Author for correspondence (e-mail: sdoneill{at}ucdavis.edu)

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