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Open Access Research article

Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica

Juha Immanen1, Kaisa Nieminen2, Héctor Duchens Silva3, Fernanda Rodríguez Rojas45, Lee A Meisel45, Herman Silva3, Victor A Albert6, Torgeir R Hvidsten78 and Ykä Helariutta1*

Author Affiliations

1 Institute of Biotechnology and Department of Biosciences, University of Helsinki, FI-00014 Helsinki, Finland

2 Finnish Forest Research Institute, Vantaa Research Unit, Jokiniemenkuja 1, FI-01301 Vantaa, Finland

3 Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, Universidad de Chile, Facultad de Ciencias Agronómicas, Av. Santa Rosa 11315, 8820808 La Pintana, Santiago, Chile

4 Universidad Andres Bello, Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, República 217, 837-0146 Santiago, Chile

5 Universidad de Chile, Instituto de Nutrición y Tecnología de los Alimentos (INTA), El Líbano 5524, 7830490 Macul, Santiago, Chile

6 Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA

7 Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden

8 Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway

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BMC Genomics 2013, 14:885  doi:10.1186/1471-2164-14-885

Published: 16 December 2013

Abstract

Background

Through the diversity of cytokinin regulated processes, this phytohormone has a profound impact on plant growth and development. Cytokinin signaling is involved in the control of apical and lateral meristem activity, branching pattern of the shoot, and leaf senescence. These processes influence several traits, including the stem diameter, shoot architecture, and perennial life cycle, which define the development of woody plants. To facilitate research about the role of cytokinin in regulation of woody plant development, we have identified genes associated with cytokinin signaling and homeostasis pathways from two hardwood tree species.

Results

Taking advantage of the sequenced black cottonwood (Populus trichocarpa) and peach (Prunus persica) genomes, we have compiled a comprehensive list of genes involved in these pathways. We identified genes belonging to the six families of cytokinin oxidases (CKXs), isopentenyl transferases (IPTs), LONELY GUY genes (LOGs), two-component receptors, histidine containing phosphotransmitters (HPts), and response regulators (RRs). All together 85 Populus and 45 Prunus genes were identified, and compared to their Arabidopsis orthologs through phylogenetic analyses.

Conclusions

In general, when compared to Arabidopsis, differences in gene family structure were often seen in only one of the two tree species. However, one class of genes associated with cytokinin signal transduction, the CKI1-like family of two-component histidine kinases, was larger in both Populus and Prunus than in Arabidopsis.

Keywords:
Cytokinin signaling; Cytokinin homeostasis; Populus trichocarpa; Black cottonwood; Prunus persica; Peach