scholarly journals Characterization, Identification and Expression Profiling of Genome-Wide R-Genes in Melon and Their Putative Roles in Bacterial Fruit Blotch Resistance

2020 ◽  
Author(s):  
Md. Rafiqul Islam ◽  
Mohammad Rashed Hossain ◽  
Denison Michael Immanuel Jesse ◽  
Hee-Jeong Jung ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Plant Diseases ◽  
Economic Losses ◽  
R Genes ◽  
Qrt Pcr ◽  
Bacterial Fruit Blotch ◽  
Genome Wide ◽  
Gene Structures

Abstract Background Bacterial fruit blotch (BFB), a disease caused by Acidovorax citrulli , results in significant economic losses in melon. The causal QTLs and genes for resistance to this disease have yet to be identified. Resistance ( R )-genes play vital roles in resistance to plant diseases. Since the complete genome sequence of melon is available and genome-wide identification of R -genes has been performed for this important crop, comprehensive expression profiling may lead to the identification of putative candidate genes that function in the response to BFB. Results We identified melon accessions that are resistant and susceptible to BFB through repeated bioassays and characterized all 70 R -genes in melon, including their gene structures, chromosomal locations, domain organizations, motif distributions, and syntenic relationships. Several disease resistance-related domains were identified, including NBS, TIR, LRR, CC, RLK, and DUF domains, and the genes were categorized based on the domains of their encoded proteins. In addition, we profiled the expression patterns of the genes in melon accessions with contrasting levels of BFB resistance at 12 h, 1 d, 3 d, and 6 d after inoculation with A. citrulli via qRT-PCR. Six R -genes exhibited consistent expression patterns (MELO3C023441, MELO3C016529, MELO3C022157, MELO3C022146, MELO3C025518, and MELO3C004303), with higher expression levels in the resistant vs. susceptible accession. Conclusion We identified six putative candidate R -genes against BFB in melon. Upon functional validation, these genes could be targeted for manipulation via breeding and biotechnological approaches to improve BFB resistance in melon in the future.

scholarly journals Characterization, Identification and Expression Profiling of Genome-Wide R-Genes in Melon and Their Putative Roles in Bacterial Fruit Blotch Resistance

2020 ◽  
Author(s):  
Md. Rafiqul Islam ◽  
Mohammad Rashed Hossain ◽  
Denison Michael Immanuel Jesse ◽  
Hee-Jeong Jung ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Complete Genome Sequence ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Plant Diseases ◽  
Economic Losses ◽  
R Genes ◽  
Bacterial Fruit Blotch ◽  
Genome Wide ◽  
Gene Structures

Abstract Background: Bacterial fruit blotch (BFB), a disease caused by Acidovorax citrulli, results in significant economic losses in melon. The causal QTLs and genes for resistance to this disease have yet to be identified. Resistance (R)-genes play vital roles in resistance to plant diseases. Since the complete genome sequence of melon is available and genome-wide identification of R-genes has been performed for this important crop, comprehensive expression profiling may lead to the identification of putative candidate genes that function in the response to BFB.Results: We identified melon accessions that are resistant and susceptible to BFB through repeated bioassays and characterized all 70 R-genes in melon, including their gene structures, chromosomal locations, domain organizations, motif distributions, and syntenic relationships. Several disease resistance-related domains were identified, including NBS, TIR, LRR, CC, RLK, and DUF domains, and the genes were categorized based on the domains of their encoded proteins. In addition, we profiled the expression patterns of the genes in melon accessions with contrasting levels of BFB resistance at 12 h, 1 d, 3 d, and 6 d after inoculation with A. citrulli. Six R-genes exhibited consistent expression patterns (MELO3C023441, MELO3C016529, MELO3C022157, MELO3C022146, MELO3C025518, and MELO3C004303), with higher expression levels in the resistant vs. susceptible accession. Conclusion: We identified six putative candidate R-genes against BFB in melon. Upon functional validation, these genes could be targeted for manipulation via breeding and biotechnological approaches to improve BFB resistance in melon in the future.

scholarly journals Genome-Wide Identification of the Early Flowering 4 (ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance

2021 ◽  
Vol 12 ◽  
Author(s):  
Miaomiao Tian ◽  
Aimin Wu ◽  
Meng Zhang ◽  
Jingjing Zhang ◽  
Hengling Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Multiple Roles ◽  
Early Flowering ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Gossypium Raimondii ◽  
Spatio Temporal ◽  
Gene Structures

The early flowering 4 (ELF4) family members play multiple roles in the physiological development of plants. ELF4s participated in the plant biological clock’s regulation process, photoperiod, hypocotyl elongation, and flowering time. However, the function in the ELF4s gene is barely known. In this study, 11, 12, 21, and 22 ELF4 genes were identified from the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. There ELF4s genes were classified into four subfamilies, and members from the same subfamily show relatively conservative gene structures. The results of gene chromosome location and gene duplication revealed that segmental duplication promotes gene expansion, and the Ka/Ks indicated that the ELF4 gene family has undergone purification selection during long-term evolution. Spatio-temporal expression patterns and qRT-PCR showed that GhELF4 genes were mainly related to flower, leaf, and fiber development. Cis-acting elements analysis and qRT-PCR showed that GhELF4 genes might be involved in the regulation of abscisic acid (ABA) or light pathways. Silencing of GhELF4-1 and GhEFL3-6 significantly affected the height of cotton seedlings and reduced the resistance of cotton. The identification and functional analysis of ELF4 genes in upland cotton provide more candidate genes for genetic modification.

scholarly journals Characterization, identification and expression profiling of genome-wide R-genes in melon and their putative roles in bacterial fruit blotch resistance

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Md. Rafiqul Islam ◽  
Mohammad Rashed Hossain ◽  
Denison Michael Immanuel Jesse ◽  
Hee-Jeong Jung ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Expression Profiling ◽  
R Genes ◽  
Bacterial Fruit Blotch ◽  
Genome Wide

scholarly journals Genome-Wide Characterization of NBS-Encoding Genes in Watermelon and Their Potential Association with Gummy Stem Blight Resistance

2019 ◽  
Vol 20 (4) ◽  
pp. 902 ◽  
Author(s):  
Md Hassan ◽  
Md Rahim ◽  
Hee-Jeong Jung ◽  
Jong-In Park ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Citrullus Lanatus ◽  
Interleukin 1 ◽  
Expression Patterns ◽  
Defense Responses ◽  
Economic Losses ◽  
R Genes ◽  
Stem Blight ◽  
Gummy Stem Blight ◽  
Encoding Genes

Watermelon (Citrullus lanatus) is a nutritionally rich and economically important horticultural crop of the Cucurbitaceae family. Gummy stem blight (GSB) is a major disease of watermelon, which is caused by the fungus Didymella bryoniae, and results in substantial economic losses in terms of yield and quality. However, only a few molecular studies have focused on GSB resistance in watermelon. Nucleotide binding site (NBS)-encoding resistance (R) genes play important roles in plant defense responses to several pathogens, but little is known about the role of NBS-encoding genes in disease resistance in watermelon. The analyzed NBS-encoding R genes comprises several domains, including Toll/interleukin-1 receptor(TIR), NBS, leucine-rich repeat (LRR), resistance to powdery mildew8(RPW8) and coiled coil (CC), which are known to be involved in disease resistance. We determined the expression patterns of these R genes in resistant and susceptible watermelon lines at different time points after D. bryoniae infection by quantitative RT-PCR. The R genes exhibited various expression patterns in the resistant watermelon compared to the susceptible watermelon. Only six R genes exhibited consistent expression patterns (Cla001821, Cla019863, Cla020705, Cla012430, Cla012433 and Cla012439), which were higher in the resistant line compared to the susceptible line. Our study provides fundamental insights into the NBS-LRR gene family in watermelon in response to D. bryoniae infection. Further functional studies of these six candidate resistance genes should help to advance breeding programs aimed at improving disease resistance in watermelons.

scholarly journals Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guang Yang ◽  
Wenqiu Pan ◽  
Ruoyu Zhang ◽  
Yan Pan ◽  
Qifan Guo ◽  
...  
Keyword(s):  
Coenzyme A ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Head Blight ◽  
Genome Wide ◽  
Genome Search ◽  
Gene Structures ◽  
Main Components ◽  
Main Regulator ◽  
Group Sharing

Abstract Background Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood. Results Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data. Conclusions This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond.

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 The bZIP gene family in watermelon: genome-wide identification and expression analysis under cold stress and root-knot nematode infection

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7878 ◽  
Author(s):  
Youxin Yang ◽  
Jingwen Li ◽  
Hao Li ◽  
Yingui Yang ◽  
Yelan Guang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Red Light ◽  
Nematode Infection ◽  
Root Knot Nematode ◽  
Basic Leucine Zipper ◽  
Genome Wide ◽  
Gene Structures ◽  
Bzip Family

The basic leucine zipper (bZIP) family transcription factors play crucial roles in regulating plant development and stress response. In this study, we identified 62 ClabZIP genes from watermelon genome, which were unevenly distributed across the 11 chromosomes. These ClabZIP proteins could be classified into 13 groups based on the phylogenetic relationships, and members in the same group showed similar compositions of conserved motifs and gene structures. Transcriptome analysis revealed that a number of ClabZIP genes have important roles in the melatonin (MT) induction of cold tolerance. In addition, some ClabZIP genes were induced or repressed under red light (RL) or root-knot nematode infection according to the transcriptome data, and the expression patterns of several ClabZIP genes were further verified by quantitative real-time PCR, revealing their possible roles in RL induction of watermelon defense against nematode infection. Our results provide new insights into the functions of different ClabZIP genes in watermelon and their roles in response to cold stress and nematode infection.

scholarly journals Genome-wide investigation of microRNAs and expression profiles during rhizome development in ginger (Zingiber officinale Roscoe)

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yuan Li ◽  
Yun Ren ◽  
Ying Zhao ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Mirna Target ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Qrt Pcr ◽  
Putative Target ◽  
Genome Wide ◽  
Ginger Rhizome ◽  
Rhizome Development

Abstract Background MicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages. Results In total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively. Conclusion This is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.

scholarly journals Genome-wide analysis of BBX gene family in Tartary buckwheat (Fagopyrum tataricum)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11939
Author(s):  
Jiali Zhao ◽  
Hongyou Li ◽  
Juan Huang ◽  
Taoxiong Shi ◽  
Ziye Meng ◽  
...  
Keyword(s):  
Growth And Development ◽  
Environmental Changes ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Tartary Buckwheat ◽  
Chromosome 6 ◽  
Fagopyrum Tataricum ◽  
Conserved Motifs ◽  
Genome Wide ◽  
Gene Structures

BBX (B-box), a zinc finger transcription factor with one or two B-box domains, plays an important role in plant photomorphogenesis, growth, and development as well as response to environmental changes. In this study, 28 Tartary buckwheat BBX (FtBBX) genes were identified and screened using a comparison program. Their physicochemical properties, gene structures, conserved motifs, distribution in chromosomal, and phylogeny of the coding proteins, as well as their expression patterns, were analyzed. In addition, multiple collinearity analysis in three monocots and three dicot species illustrated that the BBX proteins identified from monocots clustered separately from those of dicots. Moreover, the expression of 11 candidate BBX genes with probable involvement in the regulation of anthocyanin biosynthesis was analyzed in the sprouts of Tartary buckwheat during light treatment. The results of gene structure analysis showed that all the 28 BBX genes contained B-box domain, three genes lacked introns, and these genes were unevenly distributed on the other seven chromosomes except for chromosome 6. The 28 proteins contained 10 conserved motifs and could be divided into five subfamilies. BBX genes of Tartary buckwheat showed varying expression under different conditions demonstrating that FtBBXs might play important roles in Tartary buckwheat growth and development. This study lays a foundation for further understanding of Tartary buckwheat BBX genes and their functions in growth and development as well as regulation of pigmentation in Tartary buckwheat.

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