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. 2021 Nov 15;12(11):1799.
doi: 10.3390/genes12111799.

Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao

Qianqian Zhang  1 , Sijia Hou  1 , Zhenmei Sun  2 , Jing Chen  1 , Jianqiao Meng  1 , Dan Liang  1 , Rongling Wu  1 , Yunqian Guo  1
Affiliations

Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao

Qianqian Zhang et al. Genes (Basel). .

Abstract

The MADS-box family gene is a class of transcription factors that have been extensively studied and involved in several plant growth and development processes, especially in floral organ specificity, flowering time and initiation and fruit development. In this study, we identified 69 candidate MADS-box genes and clustered these genes into five subgroups (Mα: 11; Mβ: 2; Mγ: 14; Mδ: 9; MIKC: 32) based on their phylogenetical relationships with Arabidopsis. Most TcMADS genes within the same subgroup showed a similar gene structure and highly conserved motifs. Chromosomal distribution analysis revealed that all the TcMADS genes were evenly distributed in 10 chromosomes. Additionally, the cis-acting elements of promoter, physicochemical properties and subcellular localization were also analyzed. This study provides a comprehensive analysis of MADS-box genes in Theobroma cacao and lays the foundation for further functional research.

Keywords: MADS-box transcription factors; Theobroma cacao; bioinformatics analysis; gene family; genome-wide characterization.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree of MADS-box genes in Arabidopsis and Theobroma cacao. The MADS-box genes are indicated with light pink and light green shade for Arabidopsis and Theobroma cacao, respectively. In second (narrow) ring from outside, the size of the area represented by the two colors shows the proportion of genes from two species in each group. The subgroups are marked by colorful background and circles.
Figure 2
Figure 2
Phylogenetic relationship, gene structure and conserved motifs of the TcMADS genes. (A) An unrooted NJ tree (left side of the figure) obtained using the MEGA X based on coco tree MADS-box protein sequences. (B) The exon–intro structures of Theobroma cacao MADS-box genes (central of the figure) were displayed by TBtools software. (C) Conserved motif composition of the TcMADS proteins (right side). Detailed information on the ten motifs is provided in Supplementary Table S1.
Figure 3
Figure 3
(A) Physical distribution of TcMADS genes among 10 chromosomes. (B) Number of TcMADS subfamily on each chromosome.
See this image and copyright information in PMC

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