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

Additional files

Additional file 1: Table S1:

Genetic loci and gene models (transcript IDs) of Populus trichocarpa cytokinin signaling and homeostasis genes based on the genome release version 3.0 (http://www.phytozome.net/search.php?org=Org_Ptrichocarpa_v3.0 webcite). To enable comparisons with previously published Populus gene reports, we have additionally included the respective loci and gene models as they were given in the assembly version 1.1.

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Additional file 2: Table S2:

Gene models and EST support for the Prunus persica cytokinin signaling and homeostasis genes. The gene models are given as in the genome release version 1 (http://www.phytozome.net/search.php?method=Org_Ppersica webcite).

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Additional file 3: Table S3:

List of Arabidopsis genes used in the construction of the phylogenetic trees.

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Additional file 4: Figure S1:

Alignment of Populus trichocarpa (Pt), Prunus persica (Pp) and Arabidopsis cytokinin oxidase/dehydrogenases (CKXs).

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Additional file 5: Figure S2:

Alignment of Populus (Pt), Prunus (Pp) and Arabidopsis isopentenyl transferases (IPTs).

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Additional file 6: Figure S3:

Alignment of Populus (Pt), Prunus (Pp) and Arabidopsis LONELY GUY (LOG) proteins).

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Additional file 7: Figure S4:

Alignment of Populus (Pt), Prunus (Pp) and Arabidopsis CRE1- and CKI1-like two-component histidine kinase, together with Arabidopsis ethylene receptors (ETR1, ETR2, ERS1, ERS2 and EIN4), phytochromes (PHYA-E), a putative osmosensor (AtHK1), and the histidine kinase CKI2/AHK5.

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Additional file 8: Figure S5:

Alignment of Populus (Pt), Prunus (Pp) and Arabidopsis histidine phosphotransfer proteins (HPts). The consensus HQxKGSSxS motif, containing the phospho-accepting histidine residue (H), is marked above the alignment. Altogether four Populus (PtHPt6a, PtHP6b, PHP4b, and PtHP-like), and two Prunus (PpHP6 and PpHP-like) HPts lack the conserved histidine residue.

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Additional file 9: Figure S6:

Alignment of Populus (Pt), Prunus (Pp) and Arabidopsis response regulators (RRs).

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