scholarly journals Heat shock transcription factor (Hsf) gene family in common bean (Phaseolus vulgaris): genome-wide identification, phylogeny, evolutionary expansion and expression analyses at the sprout stage under abiotic stress

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Zhang ◽  
Jing Geng ◽  
Yanli Du ◽  
Qiang Zhao ◽  
Wenjing Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Heat Shock ◽  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Gene Structure ◽  
Expression Patterns ◽  
Economic Value ◽  
Heavy Metal Stress ◽  
Biotic And Abiotic Stress

Abstract Background Common bean (Phaseolus vulgaris) is an essential crop with high economic value. The growth of this plant is sensitive to environmental stress. Heat shock factor (Hsf) is a family of antiretroviral transcription factors that regulate plant defense system against biotic and abiotic stress. To date, few studies have identified and bio-analyzed Hsfs in common bean. Results In this study, 30 Hsf transcription factors (PvHsf1–30) were identified from the PFAM database. The PvHsf1–30 belonged to 14 subfamilies with similar motifs, gene structure and cis-acting elements. The Hsf members in Arabidopsis, rice (Oryza sativa), maize (Zea mays) and common bean were classified into 14 subfamilies. Collinearity analysis showed that PvHsfs played a role in the regulation of responses to abiotic stress. The expression of PvHsfs varied across different tissues. Moreover, quantitative real-time PCR (qRT-PCR) revealed that most PvHsfs were differentially expressed under cold, heat, salt and heavy metal stress, indicating that PvHsfs might play different functions depending on the type of abiotic stress. Conclusions In this study, we identified 30 Hsf transcription factors and determined their location, motifs, gene structure, cis-elements, collinearity and expression patterns. It was found that PvHsfs regulates responses to abiotic stress in common bean. Thus, this study provides a basis for further analysis of the function of PvHsfs in the regulation of abiotic stress in common bean.

scholarly journals Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress

2019 ◽  
Vol 20 (22) ◽  
pp. 5676 ◽  
Author(s):  
Haifeng Yan ◽  
Mingzhi Li ◽  
Yuping Xiong ◽  
Jianming Wu ◽  
Jaime A. Teixeira da Silva ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Sequences ◽  
Santalum Album ◽  
Biotic And Abiotic Stress ◽  
Functional Identification ◽  
Wrky Protein

WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.

scholarly journals Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shutao He ◽  
Xiaomeng Hao ◽  
Shuli He ◽  
Xiaoge Hao ◽  
Xiaonan Chen
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Gene Family ◽  
Sweet Potato ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Promoters ◽  
Biotic And Abiotic Stress ◽  
Protein Motifs ◽  
Genome Wide

Abstract Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

scholarly journals Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mingjia Tang ◽  
Liang Xu ◽  
Yan Wang ◽  
Wanwan Cheng ◽  
Xiaobo Luo ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Heat Shock ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Raphanus Sativus ◽  
Expression Patterns ◽  
Protein Domain ◽  
Evolutionary Analysis ◽  
Heat Shock Transcription Factors

Abstract Background Abiotic stresses due to climate change pose a great threat to crop production. Heat shock transcription factors (HSFs) are vital regulators that play key roles in protecting plants against various abiotic stresses. Therefore, the identification and characterization of HSFs is imperative to dissect the mechanism responsible for plant stress responses. Although the HSF gene family has been extensively studied in several plant species, its characterization, evolutionary history and expression patterns in the radish (Raphanus sativus L.) remain limited. Results In this study, 33 RsHSF genes were obtained from the radish genome, which were classified into three main groups based on HSF protein domain structure. Chromosomal localization analysis revealed that 28 of 33 RsHSF genes were located on nine chromosomes, and 10 duplicated RsHSF genes were grouped into eight gene pairs by whole genome duplication (WGD). Moreover, there were 23 or 9 pairs of orthologous HSFs were identified between radish and Arabidopsis or rice, respectively. Comparative analysis revealed a close relationship among radish, Chinese cabbage and Arabidopsis. RNA-seq data showed that eight RsHSF genes including RsHSF-03, were highly expressed in the leaf, root, cortex, cambium and xylem, indicating that these genes might be involved in plant growth and development. Further, quantitative real-time polymerase chain reaction (RT-qPCR) indicated that the expression patterns of 12 RsHSF genes varied upon exposure to different abiotic stresses including heat, salt, and heavy metals. These results indicated that the RsHSFs may be involved in abiotic stress response. Conclusions These results could provide fundamental insights into the characteristics and evolution of the HSF family and facilitate further dissection of the molecular mechanism responsible for radish abiotic stress responses.

scholarly journals Genome- wide characterization, expression profile analysis of WRKY family genes in Santalum album  and functional identification of their role in abiotic stress

2019 ◽  
Author(s):  
Haifeng Yan ◽  
Mingzhi Li ◽  
Yuping Xiong ◽  
Yueya Zhang ◽  
Hanzhi Liang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Sequences ◽  
Santalum Album ◽  
Biotic And Abiotic Stress ◽  
Functional Identification ◽  
Wrky Protein

Abstract Background: WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis , rice and poplar. However, knowledge on WRKY transcription factors in S antalum album is scarce. Results: Based on S . albu m genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis . Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone) while the remaining four genes were weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was stimulated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 34 and 19 SaWRKY genes, respectively were significantly induced. The function of SaWRKY1 , which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis . Conclusions: Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in development and in SA- and MeJA-mediated stress responses.

scholarly journals Genome-Wide Transcriptomic Identification and Functional Insight of Lily WRKY Genes Responding to Botrytis Fungal Disease

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 776
Author(s):  
Shipra Kumari ◽  
Bashistha Kumar Kanth ◽  
Ju young Ahn ◽  
Jong Hwa Kim ◽  
Geung-Joo Lee
Keyword(s):  
Abiotic Stress ◽  
Biotic Stress ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Lilium Longiflorum ◽  
Biotic And Abiotic Stress ◽  
Biotic Stresses ◽  
Genome Wide

Genome-wide transcriptome analysis using RNA-Seq of Lilium longiflorum revealed valuable genes responding to biotic stresses. WRKY transcription factors are regulatory proteins playing essential roles in defense processes under environmental stresses, causing considerable losses in flower quality and production. Thirty-eight WRKY genes were identified from the transcriptomic profile from lily genotypes, exhibiting leaf blight caused by Botrytis elliptica. Lily WRKYs have a highly conserved motif, WRKYGQK, with a common variant, WRKYGKK. Phylogeny of LlWRKYs with homologous genes from other representative plant species classified them into three groups- I, II, and III consisting of seven, 22, and nine genes, respectively. Base on functional annotation, 22 LlWRKY genes were associated with biotic stress, nine with abiotic stress, and seven with others. Sixteen unique LlWRKY were studied to investigate responses to stress conditions using gene expression under biotic and abiotic stress treatments. Five genes—LlWRKY3, LlWRKY4, LlWRKY5, LlWRKY10, and LlWRKY12—were substantially upregulated, proving to be biotic stress-responsive genes in vivo and in vitro conditions. Moreover, the expression patterns of LlWRKY genes varied in response to drought, heat, cold, and different developmental stages or tissues. Overall, our study provides structural and molecular insights into LlWRKY genes for use in the genetic engineering in Lilium against Botrytis disease.

scholarly journals The DUB family in Populus: identification, characterization, evolution and expression patterns

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenqing Zheng ◽  
Liang Du
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Structure ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Foliar Spray ◽  
Regulatory Elements ◽  
Limited Information ◽  
Abiotic Stress Response

Abstract Background The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. Results In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. Conclusions The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.

CCCH Zinc Finger Genes in Barley: Genome-Wide Identification, Evolution, Expression and Haplotype Analysis

2021 ◽  
Author(s):  
Qi Ai ◽  
Wenqiu Pan ◽  
Yan Zeng ◽  
Yihan Li ◽  
Licao Cui
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Zinc Finger ◽  
Molecular Breeding ◽  
Animal Feed ◽  
Expression Profiles ◽  
Exome Capture ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Developmental Processes

Abstract Background: CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. Results: In this study, a total of 35 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into seven subfamilies according to their distinct features, and this classification was supported by intron–exon structure and conserved motif analysis. Despite the large genome size of barley, the lower number of CCCH genes in barley might be attributed to the low frequency of segmental and tandem duplication events. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The expression of HvC3H9 was significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make it an excellent target for the molecular breeding of barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Conclusion: Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

scholarly journals Genome-Wide Identification of WRKY Family Genes and Analysis of Their Expression in Response to Abiotic Stress in Ginkgo biloba L.

2019 ◽  
Vol 47 (4) ◽  
pp. 1100-1115 ◽  
Author(s):  
Shuiyuan CHENG ◽  
Xiaomeng LIU ◽  
Yongling LIAO ◽  
Weiwei ZHANG ◽  
Jiabao YE ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Ginkgo Biloba ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Induced Response ◽  
Digital Object Identifier ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
Response Modes ◽  
Wrky Proteins

Ginkgo biloba is widely planted, and the extracts of leaves contain flavonoids, terpene esters and other medicinal active ingredients. WRKY proteins are a large transcription factor family in plants, which play an important role in the regulation of plant secondary metabolism and development, as well as the response to biotic and abiotic stress. In our study, we identified 40 genes with conserved WRKY motifs in the G. biloba genome and classified into groups I (groups I-N and -C), II (groups IIa, b, c, d, and e), and III, which include 12, 26, and 2 GbWRKY genes, respectively. Meanwhile, the expression patterns of 10 GbWRKY (GbWRKY2, GbWRKY3, GbWRKY5, GbWRKY7, GbWRKY11, GbWRKY15, GbWRKY23, GbWRKY29, GbWRKY31, GbWRKY32) under different tissue and abiotic stress conditions were analyzed. Under stress treatment, the expression patterns of 10 WRKY genes were changed. 10 ginkgo WRKY transcription factors were induced by ETH and SA, but there are two different induced response modes. The expression of 10 WRKY genes was inhibited under low temperature, high temperature and MeJA hormone induction. Most WRKY genes were up-regulated under the induction of high salt and ABA. GbWRKYs were differentially expressed in various tissues after abiotic stress and plant hormone treatments, thereby indicating their possible roles in biological processes and abiotic stress tolerance and adaptation. Our results provided insight into the genome-wide identification of GbWRKYs, as well as their differential responses to stresses and hormones. These data can also be utilized to identify potential molecular targets to confer tolerance to various stresses in G. biloba.   ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 4, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********

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