scholarly journals Genome-Wide Identification, Expression Profile of the TIFY Gene Family in Brassica oleracea var. capitata, and Their Divergent Response to Various Pathogen Infections and Phytohormone Treatments

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 127 ◽  
Author(s):  
Xing Liu ◽  
Cunbao Zhao ◽  
Limei Yang ◽  
Yangyong Zhang ◽  
Yong Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Oleracea ◽  
Xanthomonas Campestris ◽  
Plasmodiophora Brassicae ◽  
Specific Gene ◽  
Biological Processes ◽  
Genome Wide ◽  
Meja Treatment ◽  
Organ Specific ◽  
Divergent Response

TIFY, a plant-specific gene family with the conserved motif TIF[F/Y]XG, plays important roles in various plant biological processes. Here, a total of 36 TIFY genes were identified in the Brassica oleracea genome and classified into JAZ (22 genes), TIFY (7 genes), ZML (5 genes), and PPD (2 genes) subfamilies based on their conserved motifs, which were distributed unevenly across nine chromosomes with different lengths (339–1077 bp) and exon numbers (1–8). Following phylogenetic analysis with A. thaliana and B. rapa TIFY proteins, ten clades were obtained. The expression of these TIFY genes was organ-specific, with thirteen JAZ genes and two PPD genes showing the highest expression in roots and leaves, respectively. More importantly, the JAZs showed divergent responses to various pathogen infections and different phytohormone treatments. Compared with the susceptible line, most JAZs were activated after Plasmodiophora brassicae infection, while there were both induced and inhibited JAZs after Fusarium oxysporum or Xanthomonas campestris infection in the resistance line, indicating their probably distinct roles in disease resistance or susceptibility. Further, the JAZs were all upregulated after MeJA treatment, but were mostly downregulated after SA/ET treatment. In summary, these results contribute to our understanding of the TIFY gene family, revealing that JAZs may play crucial and divergent roles in phytohormone crosstalk and plant defense.

scholarly journals Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Planta ◽  
2021 ◽  
Vol 253 (4) ◽  
Author(s):  
Mingzhao Zhu ◽  
Shujin Lu ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Downy Mildew ◽  
Fusarium Wilt ◽  
Black Spot ◽  
Housekeeping Genes ◽  
Chitinase Gene ◽  
Genome Wide ◽  
A Genome

Abstract Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

scholarly journals Genome-wide analysis and expression profile of the bZIP gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Zhao ◽  
Song Chen ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
Boru Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Systems Biology ◽  
Gene Family ◽  
Stress Responses ◽  
Metal Ion ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

Identification and expression analysis of E2 ubiquitin-conjugating enzymes in cucumber

2021 ◽  
Author(s):  
Wei Lai ◽  
Zhaoyang Hu ◽  
Chuxia Zhu ◽  
Yingui Yang ◽  
Shiqiang Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Biological Processes ◽  
Protein Ubiquitination ◽  
Genome Wide ◽  
Conjugating Enzymes ◽  
Gene Structures ◽  
Ubiquitin Conjugating Enzymes ◽  
Genome Wide Survey

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-wide identification and expression analysis of chitin-binding gene family in Brassica oleracea L. reveals its role in different disease resistance

2020 ◽  
Author(s):  
Mingzhao Zhu ◽  
Congcong Kong ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Oleracea ◽  
Black Spot ◽  
Chitinase Gene ◽  
Chitinase A ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Chitinase Genes ◽  
Related Proteins

Abstract Background Chitinase, a category of pathogenesis-related proteins, is thought to play an important role in defending external stress in plants. However, comprehensive analysis of chitin-binding gene family has not yet been reported in cabbage (Brassica oleracea L.), especially their roles in response to different diseases. Result in this study, A total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into two groups. They were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of colinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) found in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. In addition, under four different stresses of Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression, respectively. Conclusions Our results provide insights for further understanding the role of chitinase in host plants response to different diseases.

scholarly journals Genome-wide identification and expression analysis of the cytokinin gene family in Brassica oleracea L. reveals its role in clubroot resistance

2019 ◽  
Author(s):  
Mingzhao Zhu ◽  
Yu Ning ◽  
Longxiang Yan ◽  
Wenxue Cao ◽  
Congcong Kong ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Oleracea ◽  
Plant Immunity ◽  
Homologous Gene ◽  
Element Analysis ◽  
Clubroot Disease ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

Abstract Background: cytokinins have important functions in regulating plant growth and response to abiotic stress. cytokinin family genes have been described in several plant species, but a comprehensive analysis of the cytokinin family genes in Brassica oleracea has not been reported to date, especially their roles in dealing with the invasion of P. brassicae. Results: Cytokinins are a class of phytohormones that promote cell division and differentiation and are thought to affect plant immunity to multiple pathogens. To reveal the mechanisms of the Brassica oleracea cytokinin family genes in response to clubroot disease, a total of 36 cytokinin genes were identified using a genome-wide search method. Phylogenetic analysis classified these genes into three groups. They were distributed unevenly across nine chromosomes in B. oleracea, and 15 of them did not contain introns. The results of colinear analysis showed that each cytokinin gene in the B. oleracea genome had at least one homologous gene in the Arabidopsis genome. A cis-element analysis indicated that these genes possessed several stress response cis-elements. The heatmap of the cytokinin gene family showed that these genes were expressed in various tissues and organs. Five and eight genes were up- and downregulated, respectively, in the susceptible material after inoculation. In addition, two and one genes were up- and downregulated, respectively, in resistant material. This may indicate that these cytokinin genes play important roles in the host plant response to clubroot disease. In addition, the results provide insights for better understanding the role of cytokinin in the B. oleracea–P. brassicae interaction. Conclusions: Our results are helpful to elucidate the role of cytokinin family genes in cabbage response to infection by P. brassicae, and lay a foundation for further study on the function of these genes. Keywords: Brassica oleracea, genome-wide, cytokinin family genes, clubroot

scholarly journals Genome-wide characterization and expression analysis of GRAS gene family in pepper (Capsicum annuum L.)

2018 ◽  
Author(s):  
Liu Baoling ◽  
Sun Yan ◽  
Xue Jinai ◽  
Li Runzhi
Keyword(s):  
Gene Family ◽  
Capsicum Annuum ◽  
Biological Processes ◽  
Chromosomal Distribution ◽  
Multiple Sequence ◽  
Genome Wide ◽  
Regulation Network ◽  
Motif Composition ◽  
Pepper Genome ◽  
Gras Gene

Plant-specific GRAS transcription factors diversely participate in the regulation of multiple biological processes including growth and development, signal cross-talking and biotic/abiotic responses. However, this gene family was not characterized detailed in pepper ( Capsicum annuum L.), an economically important vegetable crop. Here, a total of 50 Ca GRAS members were identified in the pepper genome and renamed by their respective chromosomal distribution. Genomic organization revealed that most CaGRAS genes (84%) have no intron. A phylogenetic analysis was carried out using Arabidopsis thaliana to classify pepper GARS genes into at least ten subfamilies. Multiple sequence alignment showed GRAS-typical domains present in those proteins, with the members from the same phylogenetic subfamily exhibiting the similar motif composition. The presence of highly divergent N-terminus may be associated with functional specificity of each CaGRAS protein. Expression of 12 CaGRAS genes was not detected in all tissues tested, suggesting that their functions may be lost during evolution. By contrast, the rest 38 CaGRAS genes were expressed largely in several organs, showing their important roles in pepper life activities. Moreover, 21 CaGRAS genes were differentially expressed under cold, drought, salt and GA treatments, indicating that they play vital roles in response to abiotic stress in pepper. The first comprehensive analysis of GRAS gene family in the pepper genome in this study provide insights into understanding the CRAS-mediated regulation network, benefiting the genetic improvements in pepper and some other relative plants.

scholarly journals BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Akram Ali Baloch ◽  
Agha Muhammad Raza ◽  
Shahjahan Shabbir Ahmed Rana ◽  
Saad Ullah ◽  
Samiullah Khan ◽  
...  
Keyword(s):  
Gene Family ◽  
Pseudomonas Syringae ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Evolutionary Model ◽  
Phylogenetic Groups ◽  
Genome Wide ◽  
Physico Chemical ◽  
Gene Structures

AbstractCNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.

Sign in / Sign up

Export Citation Format

Share Document