Changes in genes encoding transcriptional regulators can alter development and are important components of the molecular mechanisms of morphological evolution. MADS-box genes encode transcriptional regulators of diverse and important biological functions. In plants, MADS-box genes regulate flower, fruit, leaf, and root development. Recent sequencing efforts in Arabidopsis have allowed a nearly complete sampling of the MADS-box gene family from a single plant, something that was lacking in previous phylogenetic studies. To test the long-suspected parallel between the evolution of the MADS-box gene family and the evolution of plant form, a polarized gene phylogeny is necessary. MEF2 ͉ SRF ͉ homeotic genes ͉ MADS ͉ development C hanges in genes encoding transcriptional regulators may represent the most important determinants of morphological evolution in plants and animals (1), and phylogenetic analyses provide a historical framework to identify such changes. The MADS-box genes encode a eukaryotic family of transcriptional regulators involved in diverse and important biological functions, ranging from cardiac muscle development in animals to pheromone response in yeast (2). In plants, MADS-box genes encode the three floral homeotic functions predicted by the genetic ABC model of flower organ identity (3, 4). In addition, plant MADS-box genes regulate the timing of flower initiation and flower meristem identity, as well as various aspects of ovule, fruit, leaf, and root development (4, 5).Previously identified plant MADS-box genes encode proteins that share a stereotypical MIKC structure (Fig. 1), with the highly conserved DNA-binding MADS domain at the amino terminus. The moderately conserved K domain in the central portion of these proteins has been shown to be important for protein-protein interactions and likely forms a coiled-coil structure. The MADS and K domains are linked to one another by a weakly conserved I domain, whereas a poorly conserved carboxyl-terminal (C) region may function as a trans-activation domain (4). In animals and fungi, two distinct types of MADSbox genes have been identified, the SRF-like and MEF2-like classes (ref. 2; see Fig. 1).This paper provides a hypothesis on the evolutionary history of the eukaryotic MADS-box gene family. Previous studies of eukaryotic MADS-box gene evolution, which included plant and animal sequences, provided unrooted trees useful to infer the phylogenetic relationships of the MADS-box lineages (6). These previous studies suggested that at least one MADS-box gene was present in the common ancestor of plants, animals, and fungi, and that probably the duplication that gave rise to the animal MEF2-and SRF-like genes occurred after animals diverged from plants but before fungi diverged from animals (6). However, previous plant and eukaryotic studies were based on a relatively small sampling of plant MADS-box sequences for a particular species (6-9). To test whether all Arabidopsis MADSbox sequences group in a monophyletic clade distinct from all animal and fungal ...

Summary MADS‐box genes encode transcriptional regulators involved in diverse aspects of plant development. Here we describe the cloning and mRNA spatio‐temporal expression patterns of five new MADS‐box genes from Arabidopsis: AGL16, AGL18, AGL19, AGL27 and AGL31. These genes will probably become important molecular tools for both evolutionary and functional analyses of vegetative structures. We mapped our data and previous expression patterns onto a new MADS‐box phylogeny. These analyses suggest that the evolution of the MADS‐box family has involved a rapid and simultaneous functional diversification in vegetative as well as reproductive structures. The hypothetical ancestral genes had broader expression patterns than more derived ones, which have been co‐opted for putative specialized functions as suggested by their expression patterns. AGL27 and AGL31, which are closely related to the recently described flowering‐time gene FLC (previously AGL25), are expressed in most plant tissues. AGL19 is specifically expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. AGL18, which is most similar in sequence to the embryo‐expressed AGL15 gene, is expressed in the endosperm and in developing male and female gametophytes, suggesting a role for AGL18 that is distinct from previously characterized MADS‐box genes. Finally, AGL16 RNA accumulates in leaf guard cells and trichomes. Our new phylogeny reveals seven new monophyletic clades of MADS‐box sequences not specific to flowers, suggesting that complex regulatory networks involving several MADS‐box genes, similar to those that control flower development, underlie development of vegetative structures.

Although MADS-box genes involved in flower and fruit development have been well characterized, the function of MADS-box genes expressed in vegetative structures has yet to be explored. At least seven members of this family are grouped in clades of genes that are preferentially expressed in roots of Arabidopsis thaliana (L.) Heynh.. We report here the cloning of the AGL21 MADS-box gene, which belongs to the ANR1 clade, and the mRNA in situ expression patterns of this and two other root MADS-box genes. AGL17 appears to be a lateral root cap marker in the root tip, and towards the elongation zone this gene is expressed in the epidermal cells. AGL21 is highly expressed in lateral root primordia and it has a punctate expression pattern in the primary root meristem. AGL12 also has a punctate expression pattern in the primary root meristem. AGL12 and AGL21 are also expressed in the central cylinder of differentiated roots and both are expressed in developing embryos. This study, combined with previous phylogenetic analyses, indicates that these MADS-box genes may play distinct regulatory roles during root development.

MADS-box genes encode transcriptional regulators involved in diverse aspects of plant development. Here we describe the cloning and mRNA spatio-temporal expression patterns of five new MADS-box genes from Arabidopsis: AGL16, AGL18, AGL19, AGL27 and AGL31. These genes will probably become important molecular tools for both evolutionary and functional analyses of vegetative structures. We mapped our data and previous expression patterns onto a new MADS-box phylogeny. These analyses suggest that the evolution of the MADS-box family has involved a rapid and simultaneous functional diversification in vegetative as well as reproductive structures. The hypothetical ancestral genes had broader expression patterns than more derived ones, which have been co-opted for putative specialized functions as suggested by their expression patterns. AGL27 and AGL31, which are closely related to the recently described flowering-time gene FLC (previously AGL25), are expressed in most plant tissues. AGL19 is specifically expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. AGL18, which is most similar in sequence to the embryo-expressed AGL15 gene, is expressed in the endosperm and in developing male and female gametophytes, suggesting a role for AGL18 that is distinct from previously characterized MADS-box genes. Finally, AGL16 RNA accumulates in leaf guard cells and trichomes. Our new phylogeny reveals seven new monophyletic clades of MADS-box sequences not specific to flowers, suggesting that complex regulatory networks involving several MADS-box genes, similar to those that control flower development, underlie development of vegetative structures.