Citerne Hélène L, Luo Da, Pennington R Toby, Coen Enrico, Cronk Quentin C B
Shanghai Institute of Plant Physiology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
Plant Physiol. 2003 Mar;131(3):1042-53. doi: 10.1104/pp.102.016311.
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.
豆科植物中存在许多TCP基因（具有TCP结构域的转录因子）。拟南芥（TCP1）和金鱼草（Antirrhinum majus；CYCLOIDEA）中的这类基因已被证明在发育中的花原基中不对称表达，在金鱼草中，它们是花两侧对称（两侧对称花）所必需的。因此，这些基因在豆科植物中特别有趣，豆科植物被认为是独立于其他两侧对称被子植物谱系进化出两侧对称的。通过系统基因组学方法，我们表明TCP1/CYCLOIDEA的同源物存在于豆科植物中，并且可能分为两个主要类别（LEGCYC I组和II组），这显然是早期复制的结果，并且每个类别在TCP结构域中都有一个典型的氨基酸特征。此外，豆科植物中的I组基因可分为两个亚类（LEGCYC IA和IB），这显然是蝶形花亚科豆科植物基部或更低位置附近复制的结果。大多数被研究的蝶形花亚科豆科植物都存在所有三个基因（LEGCYC IA、IB和II），这促使进一步的研究来探究这三种类型之间可能的功能差异。然而，在这三个主要基因组中，由于复制和丢失的复杂历史以及谱系分选或由于功能分化导致的异速生长（位点内速率变化），物种间旁系同源物的确切关系难以确定。结果说明了在可变基因家族中确定直系同源物的潜力和困难，而系统基因组学方法制定功能假设依赖于此。
