Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (Callicarpa americana)

Abstract

The MADS-box gene family encodes a number of transcription factors that play key roles in various plant growth and development processes from response to environmental cues to cell differentiation and organ identity, especially the floral organogenesis, as in the prominent ABCDE model of flower development. Recently, the genome of American beautyberry (Callicarpa americana) has been sequenced. It is a shrub native to the southern region of United States with edible purple-colored berries; it is a member of the Lamiaceae family, a family of medical and agricultural importance. Seventy-eight MADS-box genes were identified from 17 chromosomes of the C. americana assembled genome. Peptide sequences blast and analysis of phylogenetic relationships with MADS-box genes of Sesame indicum, Solanum lycopersicum, Arabidopsis thaliana, and Amborella trichopoda were performed. Genes were separated into 32 type I and 46 type II MADS-box genes. C. americana MADS-box genes were clustered into four groups: MIKCC, MIKC*, Mα-type, and Mγ-type, while the Mβ-type group was absent. Analysis of the gene structure revealed that from 1 to 15 exons exist in C. americana MADS-box genes. The number of exons in type II MADS-box genes (5–15) greatly exceeded the number in type I genes (1–9). The motif distribution analysis of the two types of MADS-box genes showed that type II MADS-box genes contained more motifs than type I genes. These results suggested that C. americana MADS-box genes type II had more complex structures and might have more diverse functions. The role of MIKC-type MADS-box genes in flower and fruit development was highlighted when the expression profile was analyzed in different organs transcriptomes. This study is the first genome-wide analysis of the C. americana MADS-box gene family, and the results will further support any functional and evolutionary studies of C. americana MADS-box genes and serve as a reference for related studies of other plants in the medically important Lamiaceae family.

Genome-wide identification and expression analysis of MADS-box transcription factors reveal their involvement in sex determination of hardy rubber tree (Eucommia ulmoides oliv.)

“…The 66 EuMADS TFs were categorized into two groups, i.e., Type I (M-type) with 17 members and Type II (MIKC) with 49 members (Table 1) according to phylogenetic relationships (Figure 3). Subsequently, the 17 M-type EuMADS TFs were divided into two subgroups (Mα and Mγ), but no Mβ members were found (Figure 3), same as the result from American beautyberry (Callicarpa americana L.) (Alhindi and Al-Abdallat, 2021). Additionally, conserved protein domain analysis confirmed the presence of MADS domain in all the 66 EuMADS TFs and K-box domain in most MIKC-EuMADS TFs (Figure 5), as previously reported in tomato (Wang et al, 2019), physic nut (Tang et al, 2020), and cultivated alfalfa (Dong et al, 2021).…”

“…The MADS-box TF family has been studied in certain species with bisexual flowers, e.g., tomato (137 genes) ( Wang et al, 2019 ), foxtail millet (89 genes) ( Lai et al, 2022 ) and American beautyberry (78 genes) ( Alhindi and Al-Abdallat, 2021 ), and a few species with unisexual flowers, such as litchi ( L. chinensis , 101 genes) ( Guan et al, 2021 ), hop ( H. lupulus L., 65 genes) ( Gutierrez et al, 2022 ) and Populus trichocarpa Torr. & A.…”

“…Whereas, MIKC subfamily usually possesses SRF or MEF2 domains and is divided into two lineages: MIKC * and MIKC C (superscript C means classic) ( Gutierrez et al, 2022 ). Wherein genes belong to MIKC C are the most well-studied MADS-box genes by far, they contain as many as 13 subgroups: AG/SHP, AGL6, AGL12, AGL15, ANR1, AP1, AP3/PI, FLC, SEP, SOC1, SVP, TM8, and TT16 ( Theißen et al, 2016 ; Alhindi and Al-Abdallat, 2021 ).…”

Genome-Wide Identification, Evolution, and Expression Characterization of the Pepper (Capsicum spp.) MADS-box Gene Family

“…The MADS-box family is one of the largest transcription factor families and plays an important role in growth and development, and signal transduction [ 4 , 58 ]. With the development of sequencing technology, MADS-box gene family members have been identified in a variety of plants in varying numbers, such as 107 MADS - box gene members in A. thaliana [ 7 ], 83 in Camellia sinensis [ 59 ], 44 in Nelumbo nucifera [ 60 ], 44 in Erigeron breviscapus [ 61 ], 131 in Solanum lycopersicum [ 62 ], 54 in Morella rubra [ 63 ], 42 Phyllostachys heterocycle [ 64 ], 80 in Triticum aestivum [ 65 ], 54 in Ziziphus jujuba [ 66 ], 144 in Raphanus sativus [ 67 ], 82 in Lactuca sativa [ 68 ], 160 in Brassica rapa [ 69 ], 78 in Callicarpa americana [ 70 ], and 108 in Chrysanthemum nankingense [ 71 ]. These studies indicate that MADS - box genes have undergone obvious amplification and contraction, and the number and distribution in different subfamilies are also different.…”

Stress-Inducible Overexpression of SlDDF2 Gene Improves Tolerance against Multiple Abiotic Stresses in Tomato Plant

“…Phylogenetic trees were constructed using MEGA version 10 software [18] and the amino acids sequences of SlDDf2 and selected ERF subfamily proteins from tomato and Arabidopsis from the DREB-A1 and DREB-A2 groups [19] that were retrieved from the Phytozome databases [20] were included. The retrieved sequences were aligned using the ClustalW algorithm and the alignment was used to calculate distance matrices for neighbor-joining analyses with the Kimura two-parameter model and Bootstrap analysis with 10,000 replicates was performed to test the robustness of the internal branches, as described previously by Alhindi and Al-Abdallat [21].…”