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

Tareq Alhindi,Ayed M Al-Abdallat

doi:10.3390/plants10091805

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.

Highlights

Mints (Lamiaceae) are the sixth largest family of flowering plants and include many ornamental, medical, and edible species, such as basil, rosemary, thyme, peppermint, and spearmint
Putative MADS-box genes were submitted to the simple modular architecture research tool (SMART) [26]
The absence of Mβ-type genes in these species, which are all members of the Lamiales order, is an indication of a close relationship between the Lamiacaea family (C. americana and S. indicum) and Lentibulariaceae family (U. gibba) within the Lamiales order

Summary

Introduction

Mints (Lamiaceae) are the sixth largest family of flowering plants and include many ornamental, medical, and edible species, such as basil, rosemary, thyme, peppermint, and spearmint. Full genome and transcriptome sequencing data that are available at the Mints. 2021) and separate other projects are enhancing our understanding of this important medical plant family. American beautyberry (Callicarpa americana) is known for its prominent purple fruit, and it has been reported that native Americans have used it as an insect repellent and medicinal plant [1]. Callicarpa is a representative from the early-diverging mint lineage, and it has an important phylogenetic position to study the evolution of key gene families, such as the MADS-box genes. The full genome sequence of C. americana has been published [4], providing the opportunity to conduct a comprehensive analysis of the C. americana MADS-box gene family. The identity and function of MADS-box genes in this species have not been reported in detail

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