Development of the petaloid bracts of a paleoherb species, Saururus chinensis

Saururus chinensis is a core member of Saururaceae, an ancient, perianthless (lacking petals or sepals) family of the magnoliids in the Mesangiospermae, which is important for understanding the origin and evolution of early flowers due to its unusual floral composition and petaloid bracts. To compare their transcriptomes, RNA-seq abundance analysis identified 43,463 genes that were found to be differentially expressed in S. chinensis bracts. Of these, 5,797 showed significant differential expression, of which 1,770 were up-regulated and 4,027 down-regulated in green compared to white bracts. The expression profiles were also compared using cDNA microarrays, which identified 166 additional differentially expressed genes. Subsequently, qRT-PCR was used to verify and extend the cDNA microarray results, showing that the A and B class MADS-box genes were up-regulated in the white bracts. Phylogenetic analysis was performed on putative S. chinensis A and B-class of MADS-box genes to infer evolutionary relationships within the A and B-class of MADS-box gene family. In addition, nature selection and protein interactions of B class MADS-box proteins were inferred that B-class genes free from evolutionary pressures. The results indicate that petaloid bracts display anatomical and gene expression features normally associated with petals, as found in petaloid bracts of other species, and support an evolutionarily conserved developmental program for petaloid bracts.

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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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Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum

Scientific Reports ◽

10.1038/s41598-020-77375-6 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Mahpara Fatima ◽

Xiaodan Zhang ◽

Jishan Lin ◽

Ping Zhou ◽

Dong Zhou ◽

...

Keyword(s):

Tandem Duplication ◽

Expression Profiles ◽

Structural Diversity ◽

Pcr Analysis ◽

Type I ◽

Mads Box ◽

Mads Box Genes ◽

Vegetative Development ◽

Mads Box Gene ◽

Identification And Characterization

AbstractSugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes (SOC1 and SVP) may regulate vegetative development.

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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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Suppression of B function strongly supports the modified ABCE model in Tricyrtis sp. (Liliaceae)

Scientific Reports ◽

10.1038/srep24549 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 15

Author(s):

Masahiro Otani ◽

Ahmad Sharifi ◽

Shosei Kubota ◽

Kanako Oizumi ◽

Fumi Uetake ◽

...

Keyword(s):

Transgenic Plants ◽

Molecular Mechanism ◽

Direct Evidence ◽

Mads Box ◽

Mads Box Genes ◽

Repressor Gene ◽

Organ Identity ◽

Abce Model ◽

Liliaceous Ornamental ◽

B Class Genes

Abstract B class MADS-box genes play important roles in petal and stamen development. Some monocotyledonous species, including liliaceous ones, produce flowers with petaloid tepals in whorls 1 and 2. A modified ABCE model has been proposed to explain the molecular mechanism of development of two-layered petaloid tepals. However, direct evidence for this modified ABCE model has not been reported to date. To clarify the molecular mechanism determining the organ identity of two-layered petaloid tepals, we used chimeric repressor gene-silencing technology (CRES-T) to examine the suppression of B function in the liliaceous ornamental Tricyrtis sp. Transgenic plants with suppressed B class genes produced sepaloid tepals in whorls 1 and 2 instead of the petaloid tepals as expected. In addition, the stamens of transgenic plants converted into pistil-like organs with ovule- and stigma-like structures. This report is the first to describe the successful suppression of B function in monocotyledonous species with two-layered petaloid tepals, and the results strongly support the modified ABCE model.

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MADS-box genes from perennial ryegrass differentially expressed during transition from vegetative to reproductive growth

Journal of Plant Physiology ◽

10.1078/0176-1617-01212 ◽

2004 ◽

Vol 161 (4) ◽

pp. 439-447 ◽

Cited By ~ 44

Author(s):

Klaus Petersen ◽

Thomas Didion ◽

Claus H. Andersen ◽

Klaus K. Nielsen

Keyword(s):

Perennial Ryegrass ◽

Differentially Expressed ◽

Mads Box ◽

Mads Box Genes ◽

Reproductive Growth

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ANÁLISE IN SILICO DOS GENES DA FAMÍLIA MADS-BOX EM ALFACE (Lactuca sativa L.)

DESAFIOS Revista Interdisciplinar da Universidade Federal do Tocantins ◽

10.20873/uftsuple2020-9077 ◽

2020 ◽

Vol 7 (Especial) ◽

pp. 41-54

Author(s):

Solange Ságio ◽

Micaele Rodrigues de Souza ◽

André Almeida Lima ◽

Horllys Gomes Barreto

Keyword(s):

Gene Prediction ◽

Phylogenetic Study ◽

Mads Box ◽

Mads Box Genes ◽

Breeding Programs ◽

Future Studies ◽

Lactuca Sativa L ◽

Mads Box Gene ◽

Object Of Study ◽

Flowering Process

High temperatures can negatively affect lettuce production by promoting early bolting, which leads to increased levels of latex accumulation in the leaves, causing them to become bitter. The lack of adaptation of this culture to such conditions made it an object of study for plant breeding programs, resulting in well succeeded studies. However, little is known about the genes that regulate lettuce flowering. A better understanding of the complex genic interactions involved in the process of lettuce floral initiation is of great importance, since it can enable the development of late-bolting cultivars through plant genetic transformation. MADS-box transcriptional factors are key flowering regulators and have been extensively studied during the flowering process in several species. Thus, this study aimed to identify and characterize the Lettuce MADS-box gene family through the use of bioinformatics tools. The computational analysis consisted in gene prediction, alignment, and phylogenetic analysis. 91 sequences of putative MADS-box genes were identified and characterized by a phylogenetic study of 20 MADS-box genes. Future studies comprising mutants for these genes in plant model species and in lettuce will enable a better understanding of the functions performed by these genes during lettuce flowering, as well as, a better comprehension of this process.

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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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Identification and characterization of MADS-box gene family in pigeonpea, their wild relatives and comparative phylogenetic analysis with grain legumes.

10.31220/osf.io/wsh8q ◽

2020 ◽

Author(s):

Kuldeep Kumar ◽

Harsha Srivastava ◽

Antara Das ◽

Kishor U. Tribhuvan ◽

Kumar Durgesh ◽

...

Keyword(s):

Single Copy ◽

Grain Legumes ◽

Wild Relatives ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide ◽

The Status ◽

Mads Box Gene ◽

Comparative Phylogenetic Analysis

Abstract MADS-box genes are classes of transcription factors involved in various physiological and developmental processes in plants. Here, genome wide identification of MADS-box genes was done in Cajanus cajan, identifying 102 members, classified into two different groups based on their gene structure. The gene based phylogeny of C. cajan MADS-box genes, and some grain legumes was developed to detect their gene homologs in C. cajan. The status of all these genes was analyzed in three wild relatives i.e. C. scarabaeoides, C. platycarpus and C. cajanifolius. A total of 41 MADS-box genes were found to be missing in wild type cultivars hinting towards their role in domestication and evolution. Single copy of Flowering locus C (FLC) and Short vegetative phase (SVP), while three copies of Suppressor of activation of Constans 1 (SOC1) was found to be present. One SOC1 gene i.e. CcMADS1.5 was found to be missing in all wild relatives, also forming separate clade in phylogeny, revealing its origin through duplication followed by divergence, and role in domestication. Expression profiling of major MADS-box genes involved in flowering was done in different tissues viz vegetative meristem vegetative leaf, reproductive meristem and reproductive bud. Gene based time tree of FLC and SOC1 gene dictates their divergence from Arabidopsis before 71 and 23 million year ago (mya) respectively. This study provides valuable insights into the functions, characteristics and evolution of MADS-box proteins in grain legumes with emphasis on C. cajan, which may help in further characterizing these genes.

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