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Published on February 27, 2003; 10.1104/pp.102.016311

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Received October 16, 2002
Returned for revision November 20, 2002
Accepted December 29, 2002

A Phylogenomic Investigation of CYCLOIDEA-Like TCP Genes in the Leguminosae

Hélène L. Citerne *, Da Luo , R. Toby Pennington , Enrico Coen , and Quentin C.B. Cronk

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.)

* Corresponding author; email: h.citerne{at}rbge.org.uk.

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.




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