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

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

Plants ◽

10.3390/plants10040776 ◽

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.

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

Canadian Journal of Plant Science ◽

10.1139/cjps-2020-0160 ◽

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.

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

BMC Genomics ◽

10.1186/s12864-021-08043-w ◽

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.

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Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽

10.3390/genes12010023 ◽

2020 ◽

Vol 12 (1) ◽

pp. 23

Author(s):

Antt Htet Wai ◽

Muhammad Waseem ◽

A B M Mahbub Morshed Khan ◽

Ujjal Kumar Nath ◽

Do Jin Lee ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Tolerance ◽

Solanum Lycopersicum ◽

Expression Profiling ◽

Abiotic Stress Tolerance ◽

Dependent Manner ◽

Solanum Lycopersicum L ◽

Genome Wide ◽

Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

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Genome-wide identification and expression analysis of Raffinose synthetase family in cotton

BMC Bioinformatics ◽

10.1186/s12859-021-04276-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ruifeng Cui ◽

Xiaoge Wang ◽

Waqar Afzal Malik ◽

Xuke Lu ◽

Xiugui Chen ◽

...

Keyword(s):

Abiotic Stress ◽

Expression Patterns ◽

Regulatory Elements ◽

Plant Leaves ◽

Motif Analysis ◽

Expression Levels ◽

Genome Wide ◽

Salt And Drought Stress ◽

Key Genes ◽

Stress Gene

Abstract Background The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resistance to abiotic stress in plants, specifically in the Gossypium species. Results In this study, we identified 74 RAFS genes from G. hirsutum, G. barbadense, G. arboreum and G. raimondii by using a series of bioinformatic methods. Phylogenetic analysis showed that the RAFS gene family in the four Gossypium species could be divided into four major clades; the relatively uniform distribution of the gene number in each species ranged from 12 to 25 based on species ploidy, most likely resulting from an ancient whole-genome polyploidization. Gene motif analysis showed that the RAFS gene structure was relatively conservative. Promoter analysis for cis-regulatory elements showed that some RAFS genes might be regulated by gibberellins and abscisic acid, which might influence their expression levels. Moreover, we further examined the functions of RAFS under cold, heat, salt and drought stress conditions, based on the expression profile and co-expression network of RAFS genes in Gossypium species. Transcriptome analysis suggested that RAFS genes in clade III are highly expressed in organs such as seed, root, cotyledon, ovule and fiber, and under abiotic stress in particular, indicating the involvement of genes belonging to clade III in resistance to abiotic stress. Gene co-expressed network analysis showed that GhRFS2A-GhRFS6A, GhRFS6D, GhRFS7D and GhRFS8A-GhRFS11A were key genes, with high expression levels under salt, drought, cold and heat stress. Conclusion The findings may provide insights into the evolutionary relationships and expression patterns of RAFS genes in Gossypium species and a theoretical basis for the identification of stress resistance materials in cotton.

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WRKY Proteins: Signaling and Regulation of Expression during Abiotic Stress Responses

The Scientific World JOURNAL ◽

10.1155/2015/807560 ◽

2015 ◽

Vol 2015 ◽

pp. 1-17 ◽

Cited By ~ 121

Author(s):

Aditya Banerjee ◽

Aryadeep Roychoudhury

Keyword(s):

Abiotic Stress ◽

Stress Responses ◽

Biotic Stress ◽

Abiotic Stresses ◽

Abiotic Stress Tolerance ◽

Plant Signaling ◽

Biological Functions ◽

Abiotic And Biotic Stress ◽

Regulation Of Expression ◽

Wrky Proteins

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of theWRKYgenes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

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