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

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1799
Author(s):  
Qianqian Zhang ◽  
Sijia Hou ◽  
Zhenmei Sun ◽  
Jing Chen ◽  
Jianqiao Meng ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Floral Organ ◽  
Organ Specificity ◽  
Distribution Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Chromosomal Distribution ◽  
Cis Acting ◽  
Development Processes ◽  
Mads Box Gene

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.

scholarly journals Role of MADS-box Gene in the Development of Flower Organs in Pineapple of a Typical Collective Fruit

2020 ◽  
Author(s):  
hongna zhang ◽  
Xiaolu Pan ◽  
Debao Yi ◽  
Wenqiu Lin ◽  
Xiumei Zhang
Keyword(s):  
Functional Characterization ◽  
Floral Organ ◽  
Type I ◽  
Type Ii ◽  
Mads Box ◽  
Mads Box Genes ◽  
Floral Organs ◽  
Genome Survey ◽  
Mads Box Gene ◽  
Collective Fruit

Abstract Background: MADS-box genes play crucial roles in plant vegetative and reproductive growth, especially in inflorescences, flower, and fruit. Pineapple is a typical collective fruit, and a comprehensive analysis of the MADS-box gene family in the development of floral organs of pineapple is still lacking. Results: In this study, the whole-genome survey and expression profiling of the MADS-box family in pineapple were introduced. Forty-four AcMADS genes were identified in pineapple, 39 of them were located on 18 chromosomes and five genes were distributed in five scaffolds. Twenty-two AcMADS genes were defined as 15 pairs of segmental duplication events. Syntenic analysis showed that pineapple is closely related to monocotyledon plants. Most members of the type II subfamily of AcMADS genes had higher expression levels in floral organs compared with type I subfamily, thereby suggesting that AcMADS of type II may play more crucial roles in the development of floral organs of pineapple. Six AcMADS genes have significant tissue-specificity expression, thereby suggesting that they may participate in the formation of one or more floral organs. Conclusions: Our findings not only benefit to reveal the functional characterization of MADS-box genes in the floral organ development of pineapple but also provide additional information for further understanding the formation and development collective fruit.

scholarly journals Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8019 ◽  
Author(s):  
Yanshu Qu ◽  
Changwei Bi ◽  
Bing He ◽  
Ning Ye ◽  
Tongming Yin ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Floral Organogenesis ◽  
Functional Studies ◽  
Genome Wide ◽  
Development Processes ◽  
Mads Box Gene

MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.

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

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1805
Author(s):  
Tareq Alhindi ◽  
Ayed M. Al-Abdallat
Keyword(s):  
Gene Family ◽  
Type I ◽  
Distribution Analysis ◽  
Type Ii ◽  
Mads Box ◽  
Mads Box Genes ◽  
Floral Organogenesis ◽  
Genome Wide ◽  
Organ Identity ◽  
Mads Box Gene

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.

scholarly journals Genome-Wide Identification and Expression Analysis of MIKC-Type MADS-Box Gene Family in Punica granatum L.

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1197
Author(s):  
Yujie Zhao ◽  
Honglian Zhao ◽  
Yuying Wang ◽  
Xinhui Zhang ◽  
Xueqing Zhao ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Punica Granatum ◽  
Mads Box ◽  
Mads Box Genes ◽  
Specific Expression ◽  
Cis Acting ◽  
Flower Meristem ◽  
Genome Wide ◽  
Mads Box Gene ◽  
Development Network

MADS-box is a critical transcription factor regulating the development of floral organs and plays essential roles in the growth and development of floral transformation, flower meristem determination, the development of male and female gametophytes, and fruit development. In this study, 36 MIKC-type MADS-box genes were identified in the ‘Taishanhong’ pomegranate genome. By utilizing phylogenetic analysis, 36 genes were divided into 14 subfamilies. Bioinformatics methods were used to analyze the gene structure, conserved motifs, cis-acting elements, and the protein interaction networks of the MIKC-type MADS-box family members in pomegranate, and their expressions pattern in different tissues of pomegranate were analyzed. Tissue-specific expression analysis revealed that the E-class genes (PgMADS03, PgMADS21, and PgMADS27) were highly expressed in floral tissues, while PgMADS29 was not expressed in all tissues, indicating that the functions of the E-class genes were differentiated. PgMADS15 of the C/D-class was the key gene in the development network of pomegranate flower organs, suggesting that PgMADS15 might play an essential role in the peel and inner seed coat development of pomegranate. The results in this study will provide a reference for the classification, cloning, and functional research of pomegranate MADS-box genes.

scholarly journals Genome-Wide Analysis of the MADS-Box Transcription Factor Family in Solanum lycopersicum

2019 ◽  
Vol 20 (12) ◽  
pp. 2961 ◽  
Author(s):  
Yunshu Wang ◽  
Jianling Zhang ◽  
Zongli Hu ◽  
Xuhu Guo ◽  
Shibing Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Constitutive Expression ◽  
Floral Organ ◽  
Mads Box ◽  
Mads Box Genes ◽  
Fruit Development And Ripening ◽  
Mads Box Gene

MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit development and ripening, remains obscure. To gain insight into the MADS-box genes in tomato, 131 tomato MADS-box genes were identified. These genes could be divided into five groups (Mα, Mβ, Mγ, Mδ, and MIKC) and were found to be located on all 12 chromosomes. We further analyzed the phylogenetic relationships among Arabidopsis and tomato, as well as the protein motif structure and exon–intron organization, to better understand the tomato MADS-box gene family. Additionally, owing to the role of MADS-box genes in floral organ identification and fruit development, the constitutive expression patterns of MADS-box genes at different stages in tomato development were identified. We analyzed 15 tomato MADS-box genes involved in floral organ identification and five tomato MADS-box genes related to fruit development by qRT-PCR. Collectively, our study provides a comprehensive and systematic analysis of the tomato MADS-box genes and would be valuable for the further functional characterization of some important members of the MADS-box gene family.

scholarly journals Function and Diversification of MADS-Box Genes in Rice

2006 ◽  
Vol 6 ◽  
pp. 1923-1932 ◽  
Author(s):  
Takahiro Yamaguchi ◽  
Hiro-Yuki Hirano
Keyword(s):  
Flower Development ◽  
Floral Organ ◽  
Flowering Plants ◽  
Grass Species ◽  
Mads Box ◽  
Mads Box Genes ◽  
Genetic Studies ◽  
Floral Diversity ◽  
Organ Identity ◽  
Mads Box Gene

MADS-box genes play critical roles in a number of developmental processes in flowering plants, such as specification of floral organ identity, control of flowering time, and regulation of fruit development. Because of their crucial functions in flower development, diversification of the MADS-box gene family has been suggested to be a major factor responsible for floral diversity during radiation of the flowering plants. Inflorescences and flowers in the grass species have unique structures that are distinct from those in eudicots. Thus, it is plausible that the diversification of the function of MADS-box genes may have been a key driving force in the morphological divergence of the flowers and inflorescences in the grasses. Indeed, recent progress in genetic studies has shown that MADS-box genes function in flower development inOryza sativa(rice), in support of the idea that functional diversification of the MADS-box genes was involved in evolution of the angiosperms. In this review, we summarize the functions of the major subfamilies of the MADS-box genes in rice and discuss their role in the development and evolution of rice flowers and inflorescences.

scholarly journals How different is similar – exploring development of Ceropegia sandersonii pitfall flowers to elucidate convergent evolution of floral synorganization

2020 ◽  
Author(s):  
Annemarie Heiduk ◽  
Dewi Pramanik ◽  
Marlies Spaans ◽  
Loes Gast ◽  
Nemi Dorst ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Genetic Background ◽  
Ct Scanning ◽  
Floral Organ ◽  
Floral Traits ◽  
Micro Ct ◽  
Mads Box ◽  
Mads Box Genes ◽  
X Ray ◽  
Mads Box Gene

Abstract Background: Lantern plants from the genus Ceropegia (Apocynaceae-Asclepiadoideae) have radially symmetric pitfall flowers that are an outstanding example of functional floral complexity with high synorganization of specialized organs. The evolutionary origin and development of these complex flowers is unclear, and the genetic background of floral organ formation is unknown. Flowers with similar deceptive pollination strategies and floral traits convergently evolved in non-related plant lineages. The partially bilaterally flattened trap flowers of pipevines are functionally similar to Ceropegia pitfall flowers; many orchid taxa evolved complex fully bilaterally flattened flowers with specialized organs to trap pollinators. This study is the first to investigate the genetic background of pitfall flower development in Ceropegia, and to explore (i) convergent evolution of extremely synorganized and complex flowers as well as (ii) the homology of a highly specialized floral organ, the gynostegial corona. Methods: We obtained transcriptomes from C. sandersonii early floral buds and mature sepals, petals, and gynostegia, and analyzed differential expression of selected MADS-box genes in buds and mature floral organs using RT-PCR. In addition, we studied floral ontogeny and vascularization using SEM and 3D X-ray micro-CT scanning. Results: We identified ten phases of floral development from primordia to mature flowers, and for the first time visualized the vascular system of mature Ceropegia pitfall flowers in a 3D-model. We identified 14 MADS-box gene homologs, representing all major MADS-box gene classes, in the floral transcriptomes of Ceropegia. Vascular bundle patterns, as revealed by 3D X-ray micro-CT scanning, in combination with high expression of GLOBOSA and AGAMOUS indicate a staminoid origin of this highly specialized floral organ which starts developing from stage seven onwards. Interestingly, AGAMOUS-LIKE6 was neither expressed in early floral buds nor in any mature floral organ, in line with the radial symmetry of all Ceropegia floral organs. Conclusion: We detected differential expression of MADS-box genes involved in Ceropegia floral organ identity and propose a new ABCDE-model for parachute flowers. We compare this with current models of unrelated plants with similar floral traits but (partially) bilaterally flattened flowers, i.e. Aristolochia fimbriata and Erycina pusilla. With this comparative approach we lay the foundation for understanding the genetic mechanisms driving convergent evolution of highly specialized deceptive trap flowers.

scholarly journals Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis

2018 ◽  
Author(s):  
Yanshu Qu ◽  
Changwei Bi ◽  
Bing He ◽  
Ning Ye ◽  
Tongming Yin ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Floral Organogenesis ◽  
Functional Studies ◽  
Genome Wide ◽  
Development Processes ◽  
Mads Box Gene

MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, 7 Mβ and 4 Mγ) and 38 MIKC-type (32 MIKCc and 6 MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark). This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.

scholarly journals 092 RNA Localization of a Strawberry MADS-Box Gene (SAG1) Involved in Fruit Development

HortScience ◽  
1999 ◽  
Vol 34 (3) ◽  
pp. 457C-457 ◽  
Author(s):  
Faye M. Rosin ◽  
David Hannapel
Keyword(s):  
Fruit Development ◽  
Sequence Similarity ◽  
Floral Organ ◽  
Reproductive Organ ◽  
Amino Acid Sequence Similarity ◽  
Nucleotide Sequence Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Mads Box Gene ◽  
And Control

MADS-box genes are an important family of highly conserved regulatory genes in plants, animals, and yeast. Genetic analyses have shown that plant MADS-box genes are homeotic and control both the spatial and temporal location of specific organs. While MADS-box genes have been extensively studied and characterized in floral organ development, their involvement in other developmental processes, such as fruit development, is not well understood. From a strawberry fruit cDNA library, we have identified a strawberry AGAMOUS-like MADS-box gene (SAG1) that is expressed in developing fruit, but not in leaves. This is the first MADS-box gene to be isolated from strawberry. The hypothesis guiding this research is that SAG1 plays an important role in the development of the fruit. Nucleotide sequence analysis showed that this cDNA had the highest sequence match to genes from the AGAMOUS family. Comparison of amino acid sequence similarity between SAG1 and members of this family ranged from 70 to 75% overall, and between 98% to100% within the MADS-box. Involvement in stamen and carpel identity is one function of this family of MADS-box genes. Northern hybridizations were performed in order to analyze the expression of this gene at the RNA level. RNA was extracted from various organs of Fragaria ×ananassa, c.v. Calypso. SAG1 RNA expression was specific to stamens, carpels and all stages of fruit and seed development. No expression was detected in roots, leaves, or sepals. Thus, we conclude that SAG1 RNA is involved in reproductive organ and fruit development.

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