**1. Introduction**

The MADS-box family genes encode transcription factors (TFs), which are widely distributed in eukaryotes and play fundamental roles in diverse biological functions [1]. The name MADS-box is derived from the initials of four transcription factors that were first discovered of this family: MINICHROMOSOME MAINTENANCE 1 (MCM1), AGAMOUS (AG), DEFICIENS (DEF), and SERUM RESPONSE FACTOR (SRF) [2]. Their N-terminal contains a highly conserved DNA-binding MADS-domain containing 56–60 amino acids [2]. Thus, a protein encoding the MADS-domain is referred to as a MADS-box protein. MADS-box genes are divided into two groups (type I and type II) throughout the eukaryotes [3]. Type I MADS-box transcription factors can be further classified into four subclasses (Mα, Mβ, Mγ, and Mδ) in view of the M domain of the encoded protein, while only a few type I genes have been characterized for their biological function [4]. Type II MADS-box transcription factors include the Myocyte Enhancer Factor 2-like (MEF2-like) group from animals and yeast and the plant-specific MIKC-type group. The name of the MIKC-type protein is derived from their four characteristic domains: MADS-box (M), intervening (I), keratin-like (K), and C-terminal (C) [5]. The MIKC type has been further subdivided into MIKC<sup>C</sup> and MIKC\* types based on phylogenetic relationships and structural features [4]. The functions of the type II genes, especially the MIKC<sup>C</sup> type MADS-box genes in plants, have been reported in more detail. To date, 39 MIKC<sup>C</sup> type MADS-box genes were found in *Arabidopsis thaliana* [6], and 38 MIKC<sup>C</sup> type MADS-box genes were found in rice [7].

MADS-box genes are known to play important roles in different aspects of plants growth and development. The MADS-box genes *AGAMOUS* (*AG*) of *Arabidopsis thaliana* [8] as well as *DEFICIENS* (*DEF*) of *Antirrhinum majus* [2] were found to regulate floral organ formation two decades ago. The MADS-box genes were thought to be the main participants in floral organ specificity. With the analysis of the specification of floral organ identity determination, a genetic model (ABC model) was proposed in which the different steps of floral development were determined by three classes of genes (A, B, and C) [9]. Class A genes are necessary for the formation of the sepal. The class A genes, together with class B genes, determine the development of petals. The combination of class B and C genes is necessary for stamen identity, and class C genes function alone to form carpels [10]. However, there are many phenomena that this model cannot explain. For example, the constitutive co-expression of the B class genes *PISTILLATA* (*PI*) and *APETALA3* (*AP3*) in *Arabidopsis thaliana* [11], does not change the identity of vegetative organs. Recent studies found that the ABC model is necessary but not sufficient to provide the floral organ identity function. Therefore, the model was advanced by subdivision into five different classes (A–E). Class D genes specify ovule development, while class E genes are necessary for the specification of petals, stamens, and carpels. In addition, these five classes of genes are mainly MADS-box genes [12]. In *Arabidopsis thaliana*, *APETALA1* (*AP1*) is a typical class A gene [13], *APETALA3* (*AP3*) and *PISTILLATA* (*PI*) belong to the class B genes [14], and *AGAMOUS* (*AG*) is a representative gene with class C function [15]. The *SEPALLATA* (*SEP*) genes are class E genes and include *SEP1*, *SEP2*, *SEP3,* and *SEP4* in *Arabidopsis thaliana* [16]. The class D gene was identified by the mutant phenotype of petunia, and the sequence similarity analysis demonstrated that the corresponding gene in Arabidopsis thaliana is *AGAMOUS-LIKE11* (*AGL11*) [17,18].

In addition, considerable evidence has revealed that MADS-box TFs share a potent effect on the regulation of fruit development and ripening [4]. There have been many studies on the function of *Solanum lycopersicum* MADS-box genes in fruit development and ripening. The tomato MADS-box gene *RIPENING INHIBITOR* (*RIN*) is an essential factor for fruit ripening that regulates many ripening-associated processes, including both ethylene-dependent and ethylene-independent ripening processes [19]. Moreover, the tomato MADS-box genes *AGAMOUSLIKE1* (*AGL1*) [20,21], *FRUITFULL1* (*FUL1*), and *FRUITFULL2* (*FUL2*) are Arabidopsis *SHATTERPROOF* (*SHP*) and *FRUITFUL* (*FULL*) homologues respectively [22,23], and their suppression results in a phenotype that is partially similar to the ripening-defective phenotype of *RIN* mutant fruits. In addition to crucial roles in the regulation of plant reproductive development, MADS-box genes have also been shown to take part in plant vegetative growth processes and some stress responses in different plants such as Arabidopsis [24], rice [7,25], wheat [26], and Chinese cabbage [27]. Thus, the MADS-box protein family is an important TFs family for plant growth and development that almost affects the whole process of plant growth and development, especially plant reproductive development.

The MADS-box family of model plant species has been widely studied, including snapdragon (*Antirrhinum majus*) [28], rice (*Oryza sativa)* [7], Chinese cabbage (*Brassica rapa*) [27], poplar (*Populus trichocarpa*) [29], bread wheat (*Triticum aestivumL*) [30], banana (*Musa acuminata*) [31], petunia (*Petunia hybrida*) [32], apple (*Malus domestica Borkh)* [33], and so on. Tomato (*Solanum lycopersicum*) is one of the most critical model plants for studying flower and fruit development, and the MADS-box genes of tomato were among the earliest to be investigated [34]. It has been reported that 24 tomato MIKCC-type MADS-box genes had been identified in 2006 [35]. However, there has been no report to date concerning systematic information for the tomato MADS-box gene family, and confusion in the names of these genes is problematic for future research.

To obtain a genome-wide analysis of the tomato MAD-box gene family, we sorted 131 MADS-box genes from tomato that are highly homologous to MADS-box proteins known in other plant species, analyzed their phylogenetic relationships, gene structure, and conserved motifs, determined their exon–intron organization, and predicted their chromosomal localization. Furthermore, we obtained the predictions of the expression pattern of these tomato MADS-box genes in order to predict their expression pattern. In addition, the expression pattern of some MADS-box genes related to tomato flower organ identity, fruit development, and ripening were determined by qPCR analyses in different stages of tomato development. These results provide details of the tomato MADS-box family and may be useful for more comprehensive investigations of tomato MADS-box gene family members.
