Genome-wide identification of MADS-box gene family in sacred lotus (Nelumbo nucifera) identifies a SEPALLATA homolog gene involved in floral development

Abstract Background Sacred lotus (Nelumbo nucifera) is a vital perennial aquatic ornamental plant. Its flower shape determines the horticultural and ornamental values. However, the mechanisms underlying lotus flower development are still elusive. MADS-box transcription factors are crucial in various features of plant development, especially in floral organogenesis and specification. It is still unknown how the MADS-box transcription factors regulate the floral organogenesis in lotus. Results To obtain a comprehensive insight into the functions of MADS-box genes in sacred lotus flower development, we systematically characterized members of this gene family based on the available genome information. A total of 44 MADS-box genes were identified, of which 16 type I and 28 type II genes were categorized based on the phylogenetic analysis. Furthermore, the structure of MADS-box genes and their expressional patterns were also systematically analyzed. Additionally, subcellular localization analysis showed that they are mainly localized in the nucleus, of which a SEPALLATA3 (SEP3) homolog NnMADS14 was proven to be involved in the floral organogenesis. Conclusion These results provide some fundamental information about the MADS-box gene family and their functions, which might be helpful in not only understanding the mechanisms of floral organogenesis but also breeding of high ornamental value cultivars in lotus.

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

PeerJ ◽

10.7717/peerj.8019 ◽

2019 ◽

Vol 7 ◽

pp. e8019 ◽

Cited By ~ 1

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.

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

Plants ◽

10.3390/plants10091805 ◽

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.

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Genome-Wide Analysis of the MADS-Box Gene Family in Maize: Gene Structure, Evolution, and Relationships

Genes ◽

10.3390/genes12121956 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1956

Author(s):

Da Zhao ◽

Zheng Chen ◽

Lei Xu ◽

Lijun Zhang ◽

Quan Zou

Keyword(s):

Transcription Factors ◽

Gene Family ◽

Floral Development ◽

Primary Root ◽

Family Members ◽

Protein Sequences ◽

Structure Evolution ◽

Mads Box ◽

Mads Box Genes ◽

Mads Box Gene

The MADS-box gene family is one of the largest families in plants and plays an important roles in floral development. The MADS-box family includes the SRF-like domain and K-box domain. It is considered that the MADS-box gene family encodes a DNA-binding domain that is generally related to transcription factors, and plays important roles in regulating floral development. Our study identified 211 MADS-box protein sequences in the Zea mays proteome and renamed all the genes based on the gene annotations. All the 211 MADS-box protein sequences were coded by 98 expressed genes. Phylogenetic analysis of the MADS-box genes showed that all the family members were categorized into five subfamilies: MIKC-type, Mα, Mβ, Mγ, and Mδ. Gene duplications are regarded as products of several types of errors during the period of DNA replication and reconstruction; in our study all the 98 MADS-box genes contained 22 pairs of segmentally duplicated events which were distributed on 10 chromosomes. We compared expression data in different tissues from the female spikelet, silk, pericarp aleurone, ear primordium, leaf zone, vegetative meristem, internode, endosperm crown, mature pollen, embryo, root cortex, secondary root, germination kernels, primary root, root elongation zone, and root meristem. According to analysis of gene ontology pathways, we found a total of 41 pathways in which MADS-box genes in maize are involved. All the studies we conducted provided an overview of MADS-box gene family members in maize and showed multiple functions as transcription factors. The related research of MADS-box domains has provided the theoretical basis of MADS-box domains for agricultural applications.

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

10.7287/peerj.preprints.27195 ◽

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

10.7287/peerj.preprints.27195v1 ◽

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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Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

Journal of Berry Research ◽

10.3233/jbr-200679 ◽

2021 ◽

pp. 1-15

Author(s):

Yaqiong Wu ◽

Chunhong Zhang ◽

Wenlong Wu ◽

Weilin Li ◽

Lianfei Lyu

Keyword(s):

Gene Family ◽

Fruit Ripening ◽

Fruit Development ◽

Expression Patterns ◽

Type I ◽

Black Raspberry ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide ◽

Mads Box Gene

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

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MADS-box genes of maize: frequent targets of selection during domestication

Genetics Research ◽

10.1017/s0016672310000509 ◽

2010 ◽

Vol 93 (1) ◽

pp. 65-75 ◽

Cited By ~ 32

Author(s):

QIONG ZHAO ◽

ALLISON L. WEBER ◽

MICHAEL D. MCMULLEN ◽

KATHERINE GUILL ◽

JOHN DOEBLEY

Keyword(s):

Flower Development ◽

Sequence Variation ◽

Coalescent Simulation ◽

Mads Box ◽

Mads Box Genes ◽

Agricultural Improvement ◽

Dna Sequence Variation ◽

Mads Box Gene ◽

Neutrality Tests ◽

Maize Domestication

SummaryMADS-box genes encode transcription factors that are key regulators of plant inflorescence and flower development. We examined DNA sequence variation in 32 maize MADS-box genes and 32 randomly chosen maize loci and investigated their involvement in maize domestication and improvement. Using neutrality tests and a test based on coalescent simulation of a bottleneck model, we identified eight MADS-box genes as putative targets of the artificial selection associated with domestication. According to neutrality tests, one additional MADS-box gene appears to have been under selection during modern agricultural improvement of maize. For random loci, two genes were indicated as targets of selection during domestication and four additional genes were indicated to be candidate-selected loci for maize improvement. These results suggest that MADS-box genes were more frequent targets of selection during domestication than genes chosen at random from the genome.

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Genome-wide analysis of the MADS-box gene family in cucumber

Genome ◽

10.1139/g2012-009 ◽

2012 ◽

Vol 55 (3) ◽

pp. 245-256 ◽

Cited By ~ 62

Author(s):

Lifang Hu ◽

Shiqiang Liu

Keyword(s):

Gene Family ◽

Tandem Duplication ◽

Tissue Expression ◽

Mads Box ◽

Mads Box Genes ◽

Motif Analysis ◽

Genome Wide Analysis ◽

Genome Wide ◽

Cucumber Genome ◽

Mads Box Gene

MADS-box transcription factors are known to be involved in many important processes during plant growth and development. To date, few cucumber MADS-box genes and little tissue expression profiling have been reported. Recent completion of the cucumber whole-genome sequencing has allowed genome-wide analysis of the MADS-box gene family in cucumber as well as its comparison with other species. Here, we performed comprehensive analyses of the 43 cucumber MADS-box genes and compared them with those in Arabidopsis, poplar, and grapevine. The phylogenetic analysis showed that most cucumber members were comparable with those in other species, with the exception of AG members. At the same time, the three subfamilies FLC, AGL12, and Bs were absent in the cucumber genome. The conserved motif analysis revealed that most motifs outside the MADS domain were distributed only in specific groups. The analysis of chromosomal localization suggested that tandem duplication might contribute to the MADS-box gene expansion. Expression analysis revealed that 42 of 43 cucumber MADS-box members were expressed in multiple plant tissues, thereby implying their various roles in plants.

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