Genome-Wide Identification and Expression Analysis of BBX Transcription Factors in Iris germanica L.

The family of B-box (BBX) transcription factors contains one or two B-BOX domains and sometimes also features a highly conserved CCT domain, which plays important roles in plant growth, development and stress response. Nevertheless, no systematic study of the BBX gene family in Iris germanica L. has been undertaken. In this study, a set of six BBX TF family genes from I. germanica was identified based on transcriptomic sequences, and clustered into three clades according to phylogenetic analysis. A transient expression analysis revealed that all six BBX proteins were localized in the nucleus. A yeast one-hybrid assay demonstrated that IgBBX3 has transactivational activity, while IgBBX1, IgBBX2, IgBBX4, and IgBBX5 have no transcriptional activation ability. The transcript abundance of IgBBXs in different tissues was divided into two major groups. The expression of IgBBX1, IgBBX2, IgBBX3 and IgBBX5 was higher in leaves, whereas IgBBX4 and IgBBX6 was higher in roots. The stress response patterns of six IgBBX were detected under phytohormone treatments and abiotic stresses. The results of this study lay the basis for further research on the functions of BBX gene family members in plant hormone and stress responses, which will promote their application in I. germanica breeding.

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Genome-Wide Analysis of R2R3-MYB Transcription Factors Family in The Autopolyploid Saccharum Spontaneum: An Exploration of Dominance Expression and Stress Response

10.21203/rs.3.rs-199103/v1 ◽

2021 ◽

Author(s):

Yuan Yuan ◽

Xiping Yang ◽

Mengfang Feng ◽

Hongyan Ding ◽

Khan Muhammad Tahir ◽

...

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Gene Family ◽

Expression Analysis ◽

Expression Profiling ◽

Saccharum Spontaneum ◽

Myb Gene ◽

Genome Wide ◽

Myb Genes ◽

R2r3 Myb

Abstract Background: Sugarcane (Saccharum) is the most important sugar crop in the world. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. Results: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genome and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which MYB43, MYB53, MYB65, MYB78, and MYB99 were validated by qPCR. Allelic expression dominance in the stem was more significant than that in the leaf, implying the differential expression of alleles may be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. Conclusions: A Genome-wide expression analysis demonstrated that SsMYB genes were involved in stem development and stress response. This study largely contributed to understanding the extent to which MYB transcription factors investigate regulatory mechanisms and functional divergence in sugarcane.

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Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Genes ◽

10.3390/genes12121867 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1867

Author(s):

Yan Li ◽

Xiang Li ◽

Jiatong Wei ◽

Kewei Cai ◽

Hongzhi Zhang ◽

...

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Cold Stress ◽

Gene Family ◽

Gene Families ◽

Regulatory Function ◽

Wrky Gene ◽

Wrky Transcription Factors ◽

Biotic Stresses ◽

Genome Wide

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

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Genome-Wide Identification and Expression Analysis of the bZIP Transcription Factors in the Mycoparasite Coniothyrium minitans

Microorganisms ◽

10.3390/microorganisms8071045 ◽

2020 ◽

Vol 8 (7) ◽

pp. 1045

Author(s):

Yuping Xu ◽

Yongchun Wang ◽

Huizhang Zhao ◽

Mingde Wu ◽

Jing Zhang ◽

...

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Gene Family ◽

Expression Analysis ◽

Stress Responses ◽

Leucine Zipper ◽

Coniothyrium Minitans ◽

Basic Leucine Zipper ◽

Bzip Domain ◽

Conidial Development

The basic leucine zipper (bZIP) proteins family is one of the largest and most diverse transcription factors, widely distributed in eukaryotes. However, no information is available regarding the bZIP gene family in Coniothyrium minitans, an important biocontrol agent of the plant pathogen Sclerotinia sclerotiorum. In this study, we identified 34 bZIP genes from the C. minitans genome, which were classified into 8 groups based on their phylogenetic relationships. Intron analysis showed that 28 CmbZIP genes harbored a variable number of introns, and 15 of them shared a feature that intron inserted into the bZIP domain. The intron position in bZIP domain was highly conserved, which was related to recognize the arginine (R) and could be treated as a genomic imprinting. Expression analysis of the CmbZIP genes in response to abiotic stresses indicated that they might play distinct roles in abiotic stress responses. Results showed that 22 CmbZIP genes were upregulated during the later stage of conidial development. Furthermore, transcriptome analysis indicated that CmbZIP genes are involved in different stages of mycoparasitism. Among deletion mutants of four CmbZIPs (CmbZIP07, -09, -13, and -16), only ΔCmbZIP16 mutants significantly reduced its tolerance to the oxidative stress. The other mutants exhibited no significant effects on colony morphology, mycelial growth, conidiation, and mycoparasitism. Taken together, our results suggested that CmbZIP genes play important roles in the abiotic stress responses, conidial development, and mycoparasitism. These results provide comprehensive information of the CmbZIP gene family and lay the foundation for further research on the bZIP gene family regarding their biological functions and evolutionary history.

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Genome-wide identification, phylogeny and expression analysis of HSF gene family in barley during abiotic stress response and reproductive development

Plant Gene ◽

10.1016/j.plgene.2020.100231 ◽

2020 ◽

Vol 23 ◽

pp. 100231

Author(s):

Sumit Kumar Mishra ◽

Anuj Kumar Poonia ◽

Reeku Chaudhary ◽

Vinay K. Baranwal ◽

Deepanksha Arora ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Gene Family ◽

Expression Analysis ◽

Reproductive Development ◽

Abiotic Stress Response ◽

Genome Wide

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Genome-wide characterization and expression analysis of citrus NUCLEAR FACTOR-Y (NF-Y) transcription factors identified a novel NF-YA gene involved in drought-stress response and tolerance

PLoS ONE ◽

10.1371/journal.pone.0199187 ◽

2018 ◽

Vol 13 (6) ◽

pp. e0199187 ◽

Cited By ~ 7

Author(s):

Suzam L. S. Pereira ◽

Cristina P. S. Martins ◽

Aurizangela O. Sousa ◽

Luciana R. Camillo ◽

Caroline P. Araújo ◽

...

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Stress Response ◽

Expression Analysis ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Genome Wide

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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 identification of the MAPK gene family in chickpea and expression analysis during development and stress response

Plant Gene ◽

10.1016/j.plgene.2017.12.001 ◽

2018 ◽

Vol 13 ◽

pp. 25-35 ◽

Cited By ~ 3

Author(s):

Archana Singh ◽

Onkar Nath ◽

Sujata Singh ◽

Sumit Kumar ◽

Indrakant Kumar Singh

Keyword(s):

Stress Response ◽

Gene Family ◽

Expression Analysis ◽

Genome Wide ◽

Mapk Gene

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Identification and Expression Analysis of SLAC/SLAH Gene Family in Brassica napus L.

International Journal of Molecular Sciences ◽

10.3390/ijms22094671 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4671

Author(s):

Yunyou Nan ◽

Yuyu Xie ◽

Ayub Atif ◽

Xiaojun Wang ◽

Yanfeng Zhang ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Expression Analysis ◽

Stress Responses ◽

Structural Characteristics ◽

Brassica Napus L ◽

Nitrate Treatment ◽

Genome Wide ◽

Slow Type ◽

Hormone Responses

Slow type anion channels (SLAC/SLAHs) play important roles during anion transport, growth and development, abiotic stress responses and hormone responses in plants. However, there is few report on SLAC/SLAHs in rapeseed (Brassica napus). Genome-wide identification and expression analysis of SLAC/SLAH gene family members were performed in B. napus. A total of 23 SLAC/SLAH genes were identified in B. napus. Based on the structural characteristics and phylogenetic analysis of these members, the SLAC/SLAHs could be classified into three main groups. Transcriptome data demonstrated that BnSLAH3 genes were detected in various tissues of the rapeseed and could be up-regulated by low nitrate treatment in roots. BnSLAC/SLAHs were exclusively localized on the plasma membrane in transient expression of tobacco leaves. These results will increase our understanding of the evolution and expression of the SLAC/SLAHs and provide evidence for further research of biological functions of candidates in B. napus.

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Expression Profiling of the Dof Gene Family Under Abiotic Stresses in Spinach

10.21203/rs.3.rs-140514/v1 ◽

2021 ◽

Author(s):

Hongying Yu ◽

Yaying Ma ◽

Yijing Lu ◽

Jingjing Yue ◽

Ray Ming

Keyword(s):

Transcription Factors ◽

Gene Family ◽

Stress Responses ◽

Expression Profiling ◽

Abiotic Stresses ◽

Specific Expression ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome ◽

Male Flowers

Abstract DNA-binding with one finger (Dof) transcription factors are plant-specific transcription factors involved in numerous pathways of plant development, especially in respond to abiotic stresses. Although genome-wide analysis of this gene family has been performed in many species, Dof genes in spinach have not been thoroughly analyzed. We performed a genome-wide analysis and characterization of Dof gene family in spinach. Twenty two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purify selection. Using Cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

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Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

10.21203/rs.3.rs-29695/v2 ◽

2020 ◽

Author(s):

Mohammad Aslam ◽

Kenji Sugita ◽

Yuan Qin ◽

Abidur Rahman

Keyword(s):

Stress Response ◽

Cold Stress ◽

Expression Analysis ◽

Stress Responses ◽

Auxin Signaling ◽

Potential Candidate ◽

Wild Type ◽

Gene Expressions ◽

Significant Differential Expression ◽

Genome Wide

Abstract Background: The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. Results: To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26 nt-31 nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRNAs in slr1 at 4°C compared with wild-type. Target gene expression analysis of the members from one potential candidate miRNAs, miR169 revealed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Conclusions: Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

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