Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>)
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 deve...
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| Format: | Article |
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MDPI AG
2021-08-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/9/1805 |
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| author | Tareq Alhindi Ayed M. Al-Abdallat |
| author_facet | Tareq Alhindi Ayed M. Al-Abdallat |
| author_sort | Tareq Alhindi |
| collection | DOAJ |
| description | 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 (<i>Callicarpa americana</i>) 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 <i>Lamiaceae</i> family, a family of medical and agricultural importance. Seventy-eight MADS-box genes were identified from 17 chromosomes of the <i>C. americana</i> assembled genome. Peptide sequences blast and analysis of phylogenetic relationships with MADS-box genes of <i>Sesame indicum</i>, <i>Solanum lycopersicum</i>, <i>Arabidopsis thaliana</i>, and <i>Amborella trichopoda</i> were performed. Genes were separated into 32 type I and 46 type II MADS-box genes. <i>C. americana</i> MADS-box genes were clustered into four groups: MIKC<sup>C</sup>, 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 <i>C. americana</i> 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 <i>C. americana</i> 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 <i>C. americana</i> MADS-box gene family, and the results will further support any functional and evolutionary studies of <i>C. americana</i> MADS-box genes and serve as a reference for related studies of other plants in the medically important <i>Lamiaceae</i> family. |
| first_indexed | 2024-03-10T07:17:15Z |
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| id | doaj.art-4513b6525fac440a92ccb343a77b06b1 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T07:17:15Z |
| publishDate | 2021-08-01 |
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| spelling | doaj.art-4513b6525fac440a92ccb343a77b06b12023-11-22T14:51:59ZengMDPI AGPlants2223-77472021-08-01109180510.3390/plants10091805Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>)Tareq Alhindi0Ayed M. Al-Abdallat1Department of Biological Sciences, School of Science, The University of Jordan, Amman 11942, JordanDepartment of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, JordanThe 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 (<i>Callicarpa americana</i>) 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 <i>Lamiaceae</i> family, a family of medical and agricultural importance. Seventy-eight MADS-box genes were identified from 17 chromosomes of the <i>C. americana</i> assembled genome. Peptide sequences blast and analysis of phylogenetic relationships with MADS-box genes of <i>Sesame indicum</i>, <i>Solanum lycopersicum</i>, <i>Arabidopsis thaliana</i>, and <i>Amborella trichopoda</i> were performed. Genes were separated into 32 type I and 46 type II MADS-box genes. <i>C. americana</i> MADS-box genes were clustered into four groups: MIKC<sup>C</sup>, 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 <i>C. americana</i> 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 <i>C. americana</i> 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 <i>C. americana</i> MADS-box gene family, and the results will further support any functional and evolutionary studies of <i>C. americana</i> MADS-box genes and serve as a reference for related studies of other plants in the medically important <i>Lamiaceae</i> family.https://www.mdpi.com/2223-7747/10/9/1805bioinformaticsgenome-wide assayMADS-box genesmedicinal plantplant transcription factors |
| spellingShingle | Tareq Alhindi Ayed M. Al-Abdallat Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>) Plants bioinformatics genome-wide assay MADS-box genes medicinal plant plant transcription factors |
| title | Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>) |
| title_full | Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>) |
| title_fullStr | Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>) |
| title_full_unstemmed | Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>) |
| title_short | Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry (<i>Callicarpa americana</i>) |
| title_sort | genome wide identification and analysis of the mads box gene family in american beautyberry i callicarpa americana i |
| topic | bioinformatics genome-wide assay MADS-box genes medicinal plant plant transcription factors |
| url | https://www.mdpi.com/2223-7747/10/9/1805 |
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