Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

Abstract Background The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. Results A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, eleven VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. Conclusions Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

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Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

BMC Genomics ◽

10.1186/s12864-019-6159-2 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Xiangpeng Leng ◽

Hongru Wei ◽

Xiaozhao Xu ◽

Sandip A. Ghuge ◽

Dongjie Jia ◽

...

Keyword(s):

Transcription Factors ◽

Plant Growth ◽

Fruit Development ◽

Growth And Development ◽

Expression Patterns ◽

Class Ii ◽

Plant Growth And Development ◽

Specific Expression ◽

Genome Wide ◽

Tcp Family

Abstract Background The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. Results A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, 11 VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. Conclusions Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

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Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

10.21203/rs.2.12437/v1 ◽

2019 ◽

Author(s):

Xiangpeng Leng ◽

Hongru Wei ◽

Xiaozhao Xu ◽

Sandip A. Ghuge ◽

Dongjie Jia ◽

...

Keyword(s):

Transcription Factors ◽

Plant Growth ◽

Fruit Development ◽

Growth And Development ◽

Expression Patterns ◽

Class Ii ◽

Plant Growth And Development ◽

Specific Expression ◽

Genome Wide ◽

Tcp Family

Abstract Background The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. Results A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, eleven VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. Conclusions Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

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Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

10.21203/rs.2.12437/v2 ◽

2019 ◽

Author(s):

xiangpeng leng ◽

Hongru Wei ◽

Xiaozhao Xu ◽

Sandip A. Ghuge ◽

Dongjie Jia ◽

...

Keyword(s):

Transcription Factors ◽

Plant Growth ◽

Fruit Development ◽

Growth And Development ◽

Expression Patterns ◽

Class Ii ◽

Plant Growth And Development ◽

Specific Expression ◽

Genome Wide ◽

Tcp Family

Abstract Background The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. Results A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, eleven VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. Conclusions Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

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Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

International Journal of Molecular Sciences ◽

10.3390/ijms21197180 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7180

Author(s):

Hongfeng Wang ◽

Hongjiao Jiang ◽

Yiteng Xu ◽

Yan Wang ◽

Lin Zhu ◽

...

Keyword(s):

Medicago Truncatula ◽

Expression Profiles ◽

Expression Patterns ◽

Ectopic Expression ◽

Feedback Regulation ◽

Specific Expression ◽

Systematic Analysis ◽

Model Legume ◽

Genome Wide ◽

A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

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Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

International Journal of Molecular Sciences ◽

10.3390/ijms21186594 ◽

2020 ◽

Vol 21 (18) ◽

pp. 6594

Author(s):

Shuting Zhang ◽

Qin Zhou ◽

Feng Chen ◽

Lan Wu ◽

Baojun Liu ◽

...

Keyword(s):

Transcription Factors ◽

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Leaf Morphogenesis ◽

Systematic Analysis ◽

Genome Wide ◽

A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

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Genome-wide analysis of metallothionein gene family in maize to reveal its role in development and stress resistance to heavy metal

Biological Research ◽

10.1186/s40659-021-00368-w ◽

2022 ◽

Vol 55 (1) ◽

Author(s):

Canhong Gao ◽

Kun Gao ◽

Huixian Yang ◽

Tangdan Ju ◽

Jingyi Zhu ◽

...

Keyword(s):

Heavy Metals ◽

Heavy Metal ◽

Plant Growth ◽

Stress Resistance ◽

Binding Sites ◽

Growth And Development ◽

Expression Profiles ◽

Expression Patterns ◽

Plant Growth And Development ◽

Specific Expression

Abstract Background Maize (Zea mays L.) is a widely cultivated cereal and has been used as an optimum heavy metal phytoremediation crop. Metallothionein (MT) proteins are small, cysteine-rich, proteins that play important roles in plant growth and development, and the regulation of stress response to heavy metals. However, the MT genes for maize have not been fully analyzed so far. Methods The putative ZmMT genes were identified by HMMER.The heat map of ZmMT genes spatial expression analysis was generated by using R with the log2 (FPKM + 1).The expression profiles of ZmMT genes under three kinds of heavy metal stresses were quantified by using qRT-PCR. The metallothionein proteins was aligned using MAFFT and phylogenetic analysis were constructed by ClustalX 2.1. The protein theoretical molecular weight and pI, subcellular localization, TFs binding sites, were predicted using ProtParam, PSORT, PlantTFDB, respectively. Results A total of 9 ZmMT genes were identified in the whole genome of maize. The results showed that eight of the nine ZmMT proteins contained one highly conserved metallothio_2 domain, while ZmMT4 contained a Metallothio_PEC domain. All the ZmMT proteins could be classified into three major groups and located on five chromosomes. The ZmMT promoters contain a large number of hormone regulatory elements and hormone-related transcription factor binding sites. The ZmMT genes exhibited spatiotemporal specific expression patterns in 23 tissues of maize development stages and showed the different expression patterns in response to Cu, Cd, and Pb heavy metal stresses. Conclusions We identified the 9 ZmMT genes, and explored their conserved motif, tissue expression patterns, evolutionary relationship. The expression profiles of ZmMT genes under three kinds of heavy metal stresses (Cu, Cd, Pb) were analyzed. In summary, the expression of ZmMTs have poteintial to be regulated by hormones. The specific expression of ZmMTs in different tissues of maize and the response to different heavy metal stresses are revealed that the role of MT in plant growth and development, and stress resistance to heavy metals.

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Genome-wide identification of CLE gene family and their potential roles in bolting and fruit bearing in cucumber (Cucumis sativus L.)

BMC Plant Biology ◽

10.1186/s12870-021-02900-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nannan Qin ◽

Yang Gao ◽

Xiaojing Cheng ◽

Yang Yang ◽

Jiang Wu ◽

...

Keyword(s):

Comparative Analysis ◽

Plant Growth ◽

Cucumis Sativus ◽

Growth And Development ◽

Upstream Region ◽

Signal Pathways ◽

Plant Growth And Development ◽

Specific Expression ◽

Genome Wide ◽

Proliferation And Differentiation

Abstract Background Signal peptides are essential for plant growth and development. In plants, biological processes including cell-cell communication, cellular proliferation and differentiation, cellular determination of self-incompatibility, and defensive responses, all depend heavily on peptide-signaling networks such as CLE (CLAVATA3/Embryo surrounding region-related). The CLEs are indispensable in different periods of plant growth and development, especially in maintaining the balance between proliferation and differentiation of stem cells in various meristematic tissues. The working system of CLE genes in cucumber, an important economical vegetable (Cucumis sativus L.), has not been fully studied yet. The distributional patterns of chromosome-level genome assembly in cucumber provide a fundamental basis for a genome-wide comparative analysis of CLE genes in such plants. Results A total of 26 individual CLE genes were identified in Chinese long ‘9930’ cucumber, the majority of which belong to unstable short alkaline and hydrophilic peptides. A comparative analysis showed a close relationship in the development of CLE genes among Arabidopsis thaliana, melon, and cucumber. Half of the exon-intron structures of all CsCLEs genes are single-exon genes, and motif 1, a typical CLE domain near the C-terminal functioning in signal pathways, is found in all cucumber CLE proteins but CsCLE9. The analysis of CREs (Cis-Regulatory Elements) in the upstream region of the 26 cucumber CLE genes indicates a possible relationship between CsCLE genes and certain functions of hormone response elements. Cucumber resulted closely related to Arabidopsis and melon, having seven and 15 orthologous CLE genes in Arabidopsis and melon, respectively. Additionally, the calculative analysis of a pair of orthologous genes in cucumber showed that as a part of the evolutionary process, CLE genes are undergoing a positive selection process which leads to functional differentiation. The specific expression of these genes was vigorous at the growth and development period and tissues. Cucumber gene CLV3 was overexpressed in Arabidopsis, more than half of the transformed plants in T1 generation showed the phenomena of obvious weakness of the development of growing point, no bolting, and a decreased ability of plant growth. Only two bolted strains showed that either the pod did not develop or the pod was short, and its development was significantly inferior to that in the wild type. Conclusions In this study, 26 CLE genes were identified in Chinese long ‘9930’ cucumber genome. The CLE genes were mainly composed of alkaline hydrophilic unstable proteins. The genes of the CLE family were divided into seven classes, and shared close relationships with their homologs in Arabidopsis and melon. The specific expression of these genes was evaluated in different periods of growth and tissue development, and CLV3, which the representative gene of the family, was overexpressed in Arabidopsis, suggesting that it has a role in bolting and fruit bearing in cucumber.

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Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

10.21203/rs.3.rs-307371/v1 ◽

2021 ◽

Author(s):

Khadiza Khatun ◽

Sourav Debnath ◽

Arif Hasan Khan Robin ◽

Antt Htet Wai ◽

Ujjal Kumar Nath ◽

...

Keyword(s):

Stress Response ◽

Plant Growth ◽

Gene Family ◽

Plant Development ◽

Expression Patterns ◽

Functional Characterization ◽

Flowering Plants ◽

Genome Wide ◽

A Genome ◽

Photoperiod Sensitive

Abstract BackgroundCONSTANS-like (CO-like, COL) is a putative zinc-finger transcription factor family that plays a key role in the control of flowering time in photoperiod-sensitive plants. Besides, the COL family protein is also involved in plant development, responses to stresses. However, information on plant development and stress response related function has not been previously performed in any solanaceous crop. In this study, a genome-wide analysis of COL gene family was conducted in Petunia hybrida cv. Mirage Rose to elucidate their roles in organ development and stress response.ResultsA total of 15 COL genes were identified in petunia. Based on their amino acid sequence identity and domain composition they were phylogenetically classified into three groups those are conserved among the flowering plants. Similar gene structure and motif distribution were observed in the same group. Subcellular localization assays demonstrated that all PaCOL proteins were localized in nucleus. Furthermore, differential expression patterns of PaCOL genes were observed in various tissues. The expression patterns of PaCOL genes were observed under various abiotic and phytohormone treatment to explore their relatedness in different stresses. Moreover, several stress and light-responsive cis-elements were detected for different PaCOL genes.ConclusionThe COL genes of petunia genome, those were clustered into three distinct groups, are conserved among flowering plants, were expressed in different tissues and induced under multiple abiotic stress treatments indicating their involvement in plant growth and development and stress response mechanism. This work laid the significant foundation for functional characterization of PaCOL gene family to uncover their biological roles in plant growth, development and in stress response.

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Genome-wide analysis of the DNA-binding with one zinc finger (Dof) transcription factor family in bananas

Genome ◽

10.1139/gen-2016-0081 ◽

2016 ◽

Vol 59 (12) ◽

pp. 1085-1100 ◽

Cited By ~ 7

Author(s):

Chen Dong ◽

Huigang Hu ◽

Jianghui Xie

Keyword(s):

Dna Binding ◽

Plant Growth ◽

Growth And Development ◽

Developmental Stages ◽

Expression Profiles ◽

Regulatory Elements ◽

Plant Growth And Development ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. In this study, we report a genome-wide search for Musa acuminata Dof (MaDof) genes and their expression profiles at different developmental stages and in response to various abiotic stresses. In addition, a complete overview of the Dof gene family in bananas is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences. Based on the genome-wide analysis, we identified 74 full-length protein-coding MaDof genes unevenly distributed on 11 chromosomes. Phylogenetic analysis with Dof members from diverse plant species showed that MaDof genes can be classified into four subgroups (StDof I, II, III, and IV). The detailed genomic information of the MaDof gene homologs in the present study provides opportunities for functional analyses to unravel the exact role of the genes in plant growth and development.

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