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Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Litchi chinensis

PROVIDER: GSE182447 | GEO | 2021/10/27

REPOSITORIES: GEO

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Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis II

Project description:Litchi possesses unique ﬂower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower organ development remains largely unknown. MADS-box genes are promise candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes, and can be divided into type I and type II genes. Fifty type I MADS-box genes are sub-divided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC*-type genes. Both two types of LcMADS genes mainly contain ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveals that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes including LcMADS42/46/47/75/93/100 play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS75 (LcAP1) and LcMADS51 (LcSTK). However, JA probably plays a negative role in litchi flower development.

2021-10-27 | GSE182444 | GEO

Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis I

2021-10-27 | GSE182439 | GEO

Genome-Wide Identification and Expression Analysis of MADS-Box Family Genes in Litchi (Litchi chinensis Sonn.) and Their Involvement in Floral Sex Determination.

Project description:Litchi possesses unique flower morphology and adaptive reproduction strategies. Although previous attention has been intensively devoted to the mechanisms underlying its floral induction, the molecular basis of flower sex determination remains largely unknown. MADS-box genes are promising candidates for this due to their significant roles in various aspects of inflorescence and flower organogenesis. Here, we present a detailed overview of phylogeny and expression profiles of 101 MADS-box genes that were identified in litchi. These LcMADSs are unevenly located across the 15 chromosomes and can be divided into type I and type II genes. Fifty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups, while fifty-one type II LcMADSs consist of 37 MIKCC -type and 14 MIKC *-type genes. Promoters of both types of LcMADS genes contain mainly ABA and MeJA response elements. Tissue-specific and development-related expression analysis reveal that LcMADS51 could be positively involved in litchi carpel formation, while six MADS-box genes, including LcMADS42/46/47/75/93/100, play a possible role in stamen development. GA is positively involved in the sex determination of litchi flowers by regulating the expression of LcMADS51 (LcSTK). However, JA down-regulates the expression of floral organ identity genes, suggesting a negative role in litchi flower development.

| S-EPMC8540616 | biostudies-literature

Genome-Wide Characterization and Phylogenetic and Stress Response Expression Analysis of the MADS-Box Gene Family in Litchi (Litchi chinensis Sonn.).

Project description:The MADS-box protein is an important transcription factor in plants and plays an important role in regulating the plant abiotic stress response. In this study, a total of 94 MADS-box genes were predicted in the litchi genome, and these genes were widely distributed on all the chromosomes. The LcMADS-box gene family was divided into six subgroups (Mα, Mβ, Mγ, Mδ, MIKC, and UN) based on their phylogenetical relationships with Arabidopsis, and the closely linked subgroups exhibited more similarity in terms of motif distribution and intron/exon numbers. Transcriptome analysis indicated that LcMADS-box gene expression varied in different tissues, which can be divided into universal expression and specific expression. Furthermore, we further validated that LcMADS-box genes can exhibit different responses to various stresses using quantitative real-time PCR (qRT-PCR). Moreover, physicochemical properties, subcellular localization, collinearity, and cis-acting elements were also analyzed. The findings of this study provide valuable insights into the MADS-box gene family in litchi, specifically in relation to stress response. The identification of hormone-related and stress-responsive cis-acting elements in the MADS-box gene promoters suggests their involvement in stress signaling pathways. This study contributes to the understanding of stress tolerance mechanisms in litchi and highlights potential regulatory mechanisms underlying stress responses.

| S-EPMC10855657 | biostudies-literature

Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis

Project description:Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis

| PRJNA756276 | ENA

Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis II

Project description:Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis II

| PRJNA756271 | ENA

Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis I

Project description:Genome-wide identification and expression analysis of MADS-box family genes in litchi (Litchi chinensis Sonn.) and their involvement in floral organogenesis I

| PRJNA756275 | ENA

Genome-wide analysis of MADS-box gene family in kiwifruit (Actinidia chinensis var. chinensis) and their potential role in floral sex differentiation.

Project description:Kiwifruit (Actinidia chinensis Planch.) is a functionally dioecious plant, which displays diverse morphology in male and female flowers. MADS-box is an ancient and huge gene family that plays a key role in plant floral organ differentiation. In this study, we have identified 89 MADS-box genes from A. chinensis Red 5 genome. These genes are distributed on 26 chromosomes and are classified into type I (21 genes) and type II (68 genes). Overall, type II AcMADS-box genes have more complex structures than type I with more exons, protein domains, and motifs, indicating that type II genes may have more diverse functions. Gene duplication analysis showed that most collinearity occurred in type II AcMADS-box genes, which was consistent with a large number of type II genes. Analysis of cis-acting elements in promoters showed that AcMADS-box genes are mainly associated with light and phytohormone responsiveness. The expression profile of AcMADS-box genes in different tissues showed that most genes were highly expressed in flowers. Further, the qRT-PCR analysis of the floral organ ABCDE model-related genes in male and female flowers revealed that AcMADS4, AcMADS56, and AcMADS70 were significantly expressed in female flowers. It indicated that those genes may play an important role in the sex differentiation of kiwifruit. This work provided a comprehensive analysis of the AcMADS-box genes and may help facilitate our understanding of the sex differentiation regulatory mechanism in kiwifruit.

| S-EPMC9714460 | biostudies-literature

Genome-Wide Characterization of the MADS-Box Gene Family in Radish (Raphanus sativus L.) and Assessment of Its Roles in Flowering and Floral Organogenesis.

Project description:The MADS-box gene family is an important transcription factor (TF) family that is involved in various aspects of plant growth and development, especially flowering time and floral organogenesis. Although it has been reported in many plant species, the systematic identification and characterization of MADS-box TF family is still limited in radish (Raphanus sativus L.). In the present study, a comprehensive analysis of MADS-box genes was performed, and a total of 144 MADS-box family members were identified from the whole radish genome. Meanwhile, a detailed list of MADS-box genes from other 28 plant species was also investigated. Through the phylogenetic analysis between radish and Arabidopsis thaliana, all the RsMADS genes were classified into two groups including 68 type I (31 M?, 12 M? and 25M?) and 76 type II (70 MIKCC and 6 MIKC?). Among them, 41 (28.47%) RsMADS genes were located in nine linkage groups of radish from R1 to R9. Moreover, the homologous MADS-box gene pairs were identified among radish, A. thaliana, Chinese cabbage and rice. Additionally, the expression profiles of RsMADS genes were systematically investigated in different tissues and growth stages. Furthermore, quantitative real-time PCR analysis was employed to validate expression patterns of some crucial RsMADS genes. These results could provide a valuable resource to explore the potential functions of RsMADS genes in radish, and facilitate dissecting MADS-box gene-mediated molecular mechanisms underlying flowering and floral organogenesis in root vegetable crops.

| S-EPMC5028395 | biostudies-literature

Genome-wide identification, characterization of the MADS-box gene family in Chinese jujube and their involvement in flower development.

Project description:MADS-box genes encode transcription factors that are involved in plant development control (particularly in floral organogenesis) and signal transduction pathways, though a comprehensive analysis of MADS-box family proteins in Chinese jujube (Ziziphus jujuba Mill.) is still missing. Here, we report a genome-wide analysis of the MADS-box gene family in Chinese jujube. Based on phylogenetic analyses, 52 jujube MADS-box genes were classified into 25 MIKCC-type, 3 MIKC*-type, 16 Mα, 5 Mβ and 3 Mγ genes. 37 genes were randomly distributed across all 12 putative chromosomes. We found that the type II genes are more complex than the type I genes and that tandem duplications have occurred in three groups of MADS-box genes. Meanwhile, some gene pairs in the same clade displayed similar or distinct expression profiles, suggesting possible functional redundancy or divergence. MIKCC-type genes exhibited typical temporal and spatial expression patterns in the four whorls of floral tissues. The expressions of B, C/D and E-type genes were significantly suppressed in phyllody as compared to flower, providing valuable evidence for their involvement in flower development. This study is the first comprehensive analysis of the MADS-box family in jujube, and provides valuable information for elucidating molecular regulation mechanism of jujube flower development.

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