Comparative evolutionary analysis of MADS-box genes inArabidopsisthalianaand A.lyrata

2010 ◽  
Vol 18 (2) ◽  
pp. 109 ◽  
Author(s):  
Xue Haoyue ◽  
Xu Guixia ◽  
Guo Chunce ◽  
Shan Hongyan ◽  
Kong Hongzhi
Keyword(s):  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes

scholarly journals Characteristics of banana B genome MADS-box family demonstrate their roles in fruit development, ripening, and stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yunke Zheng ◽  
Mengting Liu ◽  
Caihong Jia ◽  
Jingyi Wang ◽  
Biyu Xu ◽  
...  
Keyword(s):  
Fruit Development ◽  
Type I ◽  
Evolutionary Analysis ◽  
Banana Fruit ◽  
Type Ii ◽  
Mads Box ◽  
Mads Box Genes ◽  
Systematic Analysis ◽  
Musa Balbisiana ◽  
B Genome

AbstractMADS-box genes are critical regulators of growth and development in flowering plants. Sequencing of the Musa balbisiana (B) genome has provided a platform for the systematic analysis of the MADS-box gene family in the important banana ancestor Musa balbisiana. Seventy-seven MADS-box genes, including 18 type I and 59 type II, were strictly identified from the banana (Pisang Klutuk Wulung, PKW, 2n = 2x = 22) B genome. These genes have been preferentially placed on the banana B genome. Evolutionary analysis suggested that M. balbisiana MCM1-AGAMOUS-DEFICIENS-SRF (MbMADS) might be organized into the MIKCc, MIKC*, Mα, Mβ, and Mγ groups according to the phylogeny. MIKCc was then further categorized into 10 subfamilies according to conserved motif and gene structure analyses. The well-defined MADS-box genes highlight gene birth and death in banana. MbMADSes originated from the same ancestor as MaMADSes. Transcriptome analysis in cultivated banana (ABB) revealed that MbMADSes were conserved and differentially expressed in several organs, in various fruit developing and ripening stages, and in stress treatments, indicating the participation of these genes in fruit development, ripening, and stress responses. Of note, SEP/AGL2 and AG, as well as other several type II MADS-box genes, including the STMADS11 and TM3/SOC1 subfamilies, indicated elevated expression throughout banana fruit development, ripening, and stress treatments, indicating their new parts in controlling fruit development and ripening. According to the co-expression network analysis, MbMADS75 interacted with bZIP and seven other transcription factors to perform its function. This systematic analysis reveals fruit development, ripening, and stress candidate MbMADSes genes for additional functional studies in plants, improving our understanding of the transcriptional regulation of MbMADSes genes and providing a base for genetic modification of MADS-mediated fruit development, ripening, and stress.

scholarly journals Functional and evolutionary analysis of the AP1/SEP/AGL6 superclade of MADS-box genes in the basal eudicot Epimedium sagittatum

2014 ◽  
Vol 113 (4) ◽  
pp. 653-668 ◽  
Author(s):  
Wei Sun ◽  
Wenjun Huang ◽  
Zhineng Li ◽  
Chi Song ◽  
Di Liu ◽  
...  
Keyword(s):  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Basal Eudicot ◽  
Epimedium Sagittatum

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.

Evolutionary Diversity of Symbiotically Induced Nodule MADS Box Genes: Characterization of nmhC5, a Member of a Novel Subfamily

1997 ◽  
Vol 10 (5) ◽  
pp. 665-676 ◽  
Author(s):  
Jacqueline Heard ◽  
Michal Caspi ◽  
Kathleen Dunn
Keyword(s):  
Root Nodules ◽  
Consensus Sequence ◽  
Structural Similarity ◽  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Mads Box Gene ◽  
Dna Binding Assay

Unique organs called nodules form on legume roots in response to intracellular infection by soil bacteria in the genus Rhizobium. This study describes a new MADS box gene, nmhC5, which along with nmh7 (J. Heard and K. Dunn, Proc. Natl. Acad. Sci. USA 92:5273-5277, 1995), is expressed in alfalfa (Medicago sativa) root nodules. Together, these genes represent the first putative transcription factors identified in nodules. Expression in a root-derived structure supports the growing sentiment that MADS box proteins have diverse roles in plant development. Comparison of the putative translation product of nmhC5 with those of other reported members of the MADS box family suggests that the overall structure of nmhC5 is conserved. Evolutionary analysis among the MADS box family showed that nmhC5 is orthologous to a root-expressed clone in Arabidopsis thaliana, agl17, and that nmh7 is similar to the floral subfamily with AP3 (DefA)/PI (Glo). Consistent with a prediction of homodimer formation, NMHC5 was shown to bind a CArG consensus sequence in vitro. In contrast, NMH7, which shows structural similarity to MADS box proteins that form heterodimers, did not bind the CArG element in an in vitro DNA-binding assay, suggesting the existence of an unknown dimer partner. The root-derived MADS box genes constitute a novel subfamily of vegetatively expressed MADS box genes. The evolutionary diversity between nmh7 and nmhC5 could represent an overall mechanistic conservation between plant developmental processes or could mean that nmh7 and nmhC5 make fundamentally different contributions to the development of the nodule.

Phylogenetic and evolutionary analysis of A-, B-, C- and E-class MADS-box genes in the basal eudicot Platanus acerifolia

2011 ◽  
Vol 125 (3) ◽  
pp. 381-393 ◽  
Author(s):  
Zhineng Li ◽  
Jiaqi Zhang ◽  
Guofeng Liu ◽  
Xiaomei Li ◽  
Chen Lu ◽  
...  
Keyword(s):  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Platanus Acerifolia ◽  
Basal Eudicot

Genomewide Structural Annotation and Evolutionary Analysis of the Type I MADS-Box Genes in Plants

2003 ◽  
Vol 56 (5) ◽  
pp. 573-586 ◽  
Author(s):  
Stefanie De Bodt ◽  
Jeroen Raes ◽  
Kobe Florquin ◽  
Stephane Rombauts ◽  
Pierre Rouz� ◽  
...  
Keyword(s):  
Type I ◽  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Structural Annotation

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 Evolutionary Analysis of MIKCc-Type MADS-Box Genes in Gymnosperms and Angiosperms

2017 ◽  
Vol 8 ◽  
Author(s):  
Fei Chen ◽  
Xingtan Zhang ◽  
Xing Liu ◽  
Liangsheng Zhang
Keyword(s):  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes

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.

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