Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron

AbstractThe organogenesis and development of reproductive organs, i.e., stamen and gynoecium, are important floral characteristics that are closely related to pollinators and reproductive fitness. As a genus from Magnoliaceae, Liriodendron has only two relict species: L. chinense and L. tulipifera. Despite the similar flower shapes of these species, their natural seed-setting rates differ significantly, implying interspecies difference in floral organogenesis and development. MADS-box genes, which participate in floral organogenesis and development, remain unexplored in Liriodendron. Here, to explore the interspecies difference in floral organogenesis and development and identify MADS-box genes in Liriodendron, we examined the stamen and gynoecium primordia of the two Liriodendron species by scanning electron microscopy combined with paraffin sectioning, and then collected two types of primordia for RNA-seq. A total of 12 libraries were constructed and 42,268 genes were identified, including 35,269 reference genes and 6,999 new genes. Monoterpenoid biosynthesis was enriched in L. tulipifera. Genome-wide analysis of 32 MADS-box genes was conducted, including phylogenetic trees, exon/intron structures, and conserved motif distributions. Twenty-six genes were anchored on 17 scaffolds, and six new genes had no location information. The expression profiles of MIKC-type genes via RT-qPCR acrossing six stamen and gynoecium developmental stages indicates that the PI-like, AG/STK-like, SEP-like, and SVP-like genes may contribute to the species-specific differentiation of the organogenesis and development of reproductive organs in Liriodendron. Our findings laid the groundwork for the future exploration of the mechanism underlying on the interspecific differences in reproductive organ development and fitness in Liriodendron.

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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 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 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 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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Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid

BMC Plant Biology ◽

10.1186/s12870-019-1836-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Chunmei He ◽

Can Si ◽

Jaime A. Teixeira da Silva ◽

Mingzhi Li ◽

Jun Duan

Keyword(s):

Seed Germination ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide

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Genome-wide study of flowering-related MADS-box genes family in Cardamine hirsuta

3 Biotech ◽

10.1007/s13205-020-02521-w ◽

2020 ◽

Vol 10 (12) ◽

Author(s):

Mahmood Ghorbani Marghashi ◽

Hedayat Bagheri ◽

Mansour Gholami

Keyword(s):

Mads Box ◽

Mads Box Genes ◽

Genome Wide ◽

Genome Wide Study

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MADS-box genes are involved in floral development and evolution.

Acta Biochimica Polonica ◽

10.18388/abp.2001_3920 ◽

2001 ◽

Vol 48 (2) ◽

pp. 351-358 ◽

Cited By ~ 41

Author(s):

H Saedler ◽

A Becker ◽

K U Winter ◽

C Kirchner ◽

G Theissen

Keyword(s):

Floral Development ◽

Higher Plants ◽

Control Cell ◽

Floral Organ ◽

Reproductive Organs ◽

Mads Box ◽

Mads Box Genes ◽

Flower Bud ◽

Organ Identity ◽

Eukaryotic Organisms

MADS-box genes encode transcription factors in all eukaryotic organisms thus far studied. Plant MADS-box proteins contain a DNA-binding (M), an intervening (I), a Keratin-like (K) and a C-terminal C-domain, thus plant MADS-box proteins are of the MIKC type. In higher plants most of the well-characterized genes are involved in floral development. They control the transition from vegetative to generative growth and determine inflorescence meristem identity. They specify floral organ identity as outlined in the ABC model of floral development. Moreover, in Antirrhinum majus the MADS-box gene products DEF/GLO and PLE control cell proliferation in the developing flower bud. In this species the DEF/GLO and the SQUA proteins form a ternary complex which determines the overall "Bauplan" of the flower. Phylogenetic reconstructions of MADS-box sequences obtained from ferns, gymnosperms and higher eudicots reveal that, although ferns possess already MIKC type genes, these are not orthologous to the well characterized MADS-box genes from gymnosperms or angiosperms. Putative orthologs of floral homeotic B- and C-function genes have been identified in different gymnosperms suggesting that these genes evolved some 300-400 million years ago. Both gymnosperms and angiosperms also contain a hitherto unknown sister clade of the B-genes, which we termed Bsister. A novel hypothesis will be described suggesting that B and Bsister might be involved in sex determination of male and female reproductive organs, respectively.

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Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability

Frontiers in Genetics ◽

10.3389/fgene.2021.818880 ◽

2022 ◽

Vol 12 ◽

Author(s):

Qasim Raza ◽

Awais Riaz ◽

Rana Muhammad Atif ◽

Babar Hussain ◽

Iqrar Ahmad Rana ◽

...

Keyword(s):

Gene Family ◽

Bread Wheat ◽

Phylogenetic Analyses ◽

Rapid Evolution ◽

Wheat Genome ◽

Fine Tuning ◽

Yield Potential ◽

Mads Box ◽

Mads Box Genes ◽

Genome Wide

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that could accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

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