First published online February 27, 2003; 10.1104/pp.102.016311
Plant Physiol, March 2003, Vol. 131, pp. 1042-1053
A Phylogenomic Investigation of CYCLOIDEA-Like TCP
Genes in the Leguminosae1
Hélène L.
Citerne,*
Da
Luo,
R. Toby
Pennington,
Enrico
Coen, and
Quentin C.B.
Cronk2
Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3
5LR, United Kingdom (H.C., R.T.P., Q.C.B.C.); Institute of Cell and
Molecular Biology, University of Edinburgh, Edinburgh EH9 3JR, United
Kingdom (H.C., Q.C.B.C.); Shanghai Institute of Plant Physiology,
Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
(D.L.); and Genetics Department, John Innes Centre, Colney Lane,
Norwich NR4 7UH, United Kingdom (E.C.)
Numerous TCP genes (transcription factors with a TCP
domain) occur in legumes. Genes of this class in Arabidopsis
(TCP1) and snapdragon (Antirrhinum majus;
CYCLOIDEA) have been shown to be asymmetrically
expressed in developing floral primordia, and in snapdragon, they are
required for floral zygomorphy (bilaterally symmetrical flowers). These
genes are therefore particularly interesting in Leguminosae, a family
that is thought to have evolved zygomorphy independently from other
zygomorphic angiosperm lineages. Using a phylogenomic approach, we show
that homologs of TCP1/CYCLOIDEA occur in
legumes and may be divided into two main classes (LEGCYC group I and II), apparently the result of an early duplication, and
each class is characterized by a typical amino acid signature in the
TCP domain. Furthermore, group I genes in legumes may be divided into
two subclasses (LEGCYC IA and IB), apparently the result
of a duplication near the base of the papilionoid legumes or below.
Most papilionoid legumes investigated have all three genes present
(LEGCYC IA, IB, and II), inviting further work to investigate possible functional difference between the three types. However, within these three major gene groups, the precise
relationships of the paralogs between species are difficult to
determine probably because of a complex history of duplication and loss
with lineage sorting or heterotachy (within-site rate variation) due to
functional differentiation. The results illustrate both the potential
and the difficulties of orthology determination in variable gene
families, on which the phylogenomic approach to formulating hypotheses
of function depends.
1
This work was supported by The Carnegie Trust
for the Universities of Scotland and by the Systematics Association.
2
Present address: Botanical Garden and Centre for Plant
Research, University of British Columbia, 6804 Southwest Marine Drive, Vancouver, BC, Canada V6T 1Z4.
*
Corresponding author; e-mail h.citerne{at}rbge.org.uk; fax
44-131-248-2901.
© 2003 American Society of Plant Biologists
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