scholarly journals Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

2020 ◽  
Author(s):  
Xinyang Wu ◽  
Yuchao Lai ◽  
Lanqing Lv ◽  
Mengfei Ji ◽  
Kelei Han ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Nicotiana Benthamiana ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Arabinogalactan Proteins ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain ◽  
Plant Pathogen Interactions

Abstract Background: Nicotiana benthamiana is widely used as a model plant to study plant-pathogen interactions. Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating plant growth, development and response to abiotic stress. However, the members of FLAs in N. benthamiana and their response to plant pathogens are unknown.Results: 38 NbFLAs were identified from a genome-wide study. NbFLAs could be divided into four subclasses, and their gene structure and motif composition were conserved in each subclass. NbFLAs may be regulated by cis-acting elements such as STRE and MBS, and could possibly be the targets of transcription factors like C2H2. Quantitative real time polymerase chain reaction (RT-qPCR) results showed that selected NbFLAs were differentially expressed in different tissues. All of the selected NbFLAs were significantly downregulated following infection by turnip mosaic virus (TuMV) and most of them also by Pseudomonas syringae pv tomato (Pst) strain DC3000 (Pst DC3000), suggesting possible roles in response to pathogenic infection.Conclusions: This study systematically identified FLAs in N. benthamiana, and indicates their potential roles in response to biotic stress. The identification of NbFLAs will facilitate further studies of their role in plant immunity in N. benthamiana.

scholarly journals Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens

2020 ◽  
Author(s):  
Xinyang Wu ◽  
Yuchao Lai ◽  
Lanqing Lv ◽  
Mengfei Ji ◽  
Kelei Han ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Nicotiana Benthamiana ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Arabinogalactan Proteins ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain ◽  
Plant Pathogen Interactions

Abstract Background: Nicotiana benthamiana is widely used as a model plant to study plant-pathogen interactions. Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating plant growth, development and response to abiotic stress. However, the members of FLAs in N. benthamiana and their response to plant pathogens are unknown.Results: 38 NbFLAs were identified from a genome-wide study. NbFLAs could be divided into four subclasses, and their gene structure and motif composition were conserved in each subclass. NbFLAs may be regulated by cis-acting elements such as STRE and MBS, and may be the targets of transcription factors like C2H2. Quantitative real time polymerase chain reaction (RT-qPCR) results showed that selected NbFLAs were differentially expressed in different tissues. All of the selected NbFLAs were significantly downregulated following infection by turnip mosaic virus (TuMV) and most of them also by Pseudomonas syringae pv tomato strain DC3000 (Pst DC3000), suggesting possible roles in response to pathogenic infection.Conclusions: This study systematically identified FLAs in N. benthamiana, and indicates their potential roles in response to biotic stress. The identification of NbFLAs will facilitate further studies of their role in plant immunity in N. benthamiana.

scholarly journals Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in Nicotiana benthamiana

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shaofei Rao ◽  
Xinyang Wu ◽  
Hongying Zheng ◽  
Yuwen Lu ◽  
Jiejun Peng ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Catharanthus Roseus ◽  
Nicotiana Benthamiana ◽  
Expression Profiles ◽  
Plant Immunity ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Phylogenetic Groups ◽  
Specific Expression ◽  
Cis Acting

Abstract Background The Catharanthus roseus RLK1-like kinase (CrRLK1L) is a subfamily of the RLK gene family, and members are sensors of cell wall integrity and regulators of cell polarity growth. Recent studies have also shown that members of this subfamily are involved in plant immunity. Nicotiana benthamiana is a model plant widely used in the study of plant-pathogen interactions. However, the members of the NbCrRLK1L subfamily and their response to pathogens have not been reported. Results In this study, a total of 31 CrRLK1L members were identified in the N. benthamiana genome, and these can be divided into 6 phylogenetic groups (I-VI). The members in each group have similar exon-intron structures and conserved motifs. NbCrRLK1Ls were predicted to be regulated by cis-acting elements such as STRE, TCA, ABRE, etc., and to be the target of transcription factors such as Dof and MYB. The expression profiles of the 16 selected NbCrRLK1Ls were determined by quantitative PCR. Most NbCrRLK1Ls were highly expressed in leaves but there were different and diverse expression patterns in other tissues. Inoculation with the bacterium Pseudomonas syringae or with Turnip mosaic virus significantly altered the transcript levels of the tested genes, suggesting that NbCrRLK1Ls may be involved in the response to pathogens. Conclusions This study systematically identified the CrRLK1L members in N. benthamiana, and analyzed their tissue-specific expression and gene expression profiles in response to different pathogens and two pathogens associated molecular patterns (PAMPs). This research lays the foundation for exploring the function of NbCrRLK1Ls in plant-microbe interactions.

scholarly journals In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

2019 ◽  
Author(s):  
Tatsuya Nobori ◽  
Yiming Wang ◽  
Jingni Wu ◽  
Sara Christina Stolze ◽  
Yayoi Tsuda ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Pseudomonas Syringae ◽  
Protein Level ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Bacterial Pathogen ◽  
Bacterial Virulence ◽  
In Planta ◽  
Bacterial Gene ◽  
Global Food Security

AbstractUnderstanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.

scholarly journals Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1669
Author(s):  
Angelo De Paolis ◽  
Sofia Caretto ◽  
Angela Quarta ◽  
Gian-Pietro Di Sansebastiano ◽  
Irene Sbrocca ◽  
...  
Keyword(s):  
Artemisia Annua ◽  
Antimalarial Activity ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

scholarly journals Two Arabidopsis Homologs of Human Lysine-Specific Demethylase Function in Epigenetic Regulation of Plant Defense Responses

2021 ◽  
Vol 12 ◽  
Author(s):  
Seong Woo Noh ◽  
Ri-Ra Seo ◽  
Hee Jin Park ◽  
Ho Won Jung
Keyword(s):  
Pseudomonas Syringae ◽  
Epigenetic Regulation ◽  
Plant Immunity ◽  
Systemic Disease ◽  
Defense Responses ◽  
Plant Defense Responses ◽  
Promoter Regions ◽  
Lysine Specific Demethylase ◽  
Genome Wide ◽  
Histone H3k4

Epigenetic marks such as covalent histone modification and DNA methylation are crucial for mitotically and meiotically inherited cellular memory-based plant immunity. However, the roles of individual players in the epigenetic regulation of plant immunity are not fully understood. Here we reveal the functions of two Arabidopsis thaliana homologs of human lysine-specific demethylase1-like1, LDL1 and LDL2, in the maintenance of methyl groups at lysine 4 of histone H3 and in plant immunity to Pseudomonas syringae infection. The growth of virulent P. syringae strains was reduced in ldl1 and ldl2 single mutants compared to wild-type plants. Local and systemic disease resistance responses, which coincided with the rapid, robust transcription of defense-related genes, were more stably expressed in ldl1 ldl2 double mutants than in the single mutants. At the nucleosome level, mono-methylated histone H3K4 accumulated in ldl1 ldl2 plants genome-wide and in the mainly promoter regions of the defense-related genes examined in this study. Furthermore, in silico comparative analysis of RNA-sequencing and chromatin immunoprecipitation data suggested that several WRKY transcription factors, e.g., WRKY22/40/70, might be partly responsible for the enhanced immunity of ldl1 ldl2. These findings suggest that LDL1 and LDL2 control the transcriptional sensitivity of a group of defense-related genes to establish a primed defense response in Arabidopsis.

scholarly journals Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

2019 ◽  
Author(s):  
Tika B. Adhikari ◽  
Brian J. Knaus ◽  
Niklaus J. Grünwald ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Plant Pathogens ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Genome Wide ◽  
A Genome

ABSTRACTGenotyping by sequencing (GBS) is considered a powerful tool to discover single nucleotide polymorphisms (SNPs), which are useful to characterize closely related genomes of plant species and plant pathogens. We applied GBS to determine genome-wide variations in a panel of 187 isolates of three closely related Alternaria spp. that cause diseases on tomato and potato in North Carolina (NC) and Wisconsin (WI). To compare genetic variations, reads were mapped to both A. alternata and A. solani draft reference genomes and detected dramatic differences in SNPs among them. Comparison of A. linariae and A. solani populations by principal component analysis revealed the first (83.8% of variation) and second (8.0% of variation) components contained A. linariae from tomato in NC and A. solani from potato in WI, respectively, providing evidence of population structure. Genetic differentiation (Hedrick’s G’ST) in A. linariae populations from Haywood, Macon, and Madison counties in NC were little or no differentiated (G’ST 0.0 - 0.2). However, A. linariae population from Swain county appeared to be highly differentiated (G’ST > 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontin’s D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host.

scholarly journals Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

2021 ◽  
Vol 22 (24) ◽  
pp. 13568
Author(s):  
Zhengfu Yang ◽  
Hongmiao Jin ◽  
Junhao Chen ◽  
Caiyun Li ◽  
Jiani Wang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Expression Patterns ◽  
Carya Illinoinensis ◽  
Expression Levels ◽  
Cis Acting ◽  
Similar Expression ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Ethylene Responsive Factor

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

scholarly journals Identification and Analysis of NBS-LRR Genes in Actinidia chinensis Genome

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1350
Author(s):  
Tao Wang ◽  
Zhan-Hui Jia ◽  
Ji-Yu Zhang ◽  
Min Liu ◽  
Zhong-Ren Guo ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Plant Immunity ◽  
Domain Architecture ◽  
Bacterial Canker ◽  
Actinidia Chinensis ◽  
R Genes ◽  
Leucine Rich Repeat ◽  
Cis Acting ◽  
Important Disease

Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the most important disease resistance genes in plants. The genome sequence of kiwifruit (Actinidia chinensis) provides resources for the characterization of NBS-LRR genes and identification of new R-genes in kiwifruit. In the present study, we identified 100 NBS-LRR genes in the kiwifruit genome and they were grouped into six distinct classes based on their domain architecture. Of the 100 genes, 79 are truncated non-regular NBS-LRR genes. Except for 37 NBS-LRR genes with no location information, the remaining 63 genes are distributed unevenly across 18 kiwifruit chromosomes and 38.01% of them are present in clusters. Seventeen families of cis-acting elements were identified in the promoters of the NBS-LRR genes, including AP2, NAC, ERF and MYB. Pseudomonas syringae pv. actinidiae (pathogen of the kiwifruit bacterial canker) infection induced differential expressions of 16 detected NBS-LRR genes and three of them are involved in plant immunity responses. Our study provides insight of the NBS-LRR genes in kiwifruit and a resource for the identification of new R-genes in the fruit.

scholarly journals Dynamic Insertion of Pot3 in AvrPib Prevailing in a Field Rice Blast Population in the Philippines Led to the High Virulence Frequency Against the Resistance Gene Pib in Rice

2019 ◽  
Vol 109 (5) ◽  
pp. 870-877 ◽  
Author(s):  
Toluwase Olukayode ◽  
Berlaine Quime ◽  
Yin-Chi Shen ◽  
Mary Jeannie Yanoria ◽  
Suobing Zhang ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Rice Blast ◽  
Indica Rice ◽  
The Philippines ◽  
Avirulence Gene ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Polymerase Chain

The Magnaporthe oryzae avirulence gene AvrPib is required for the resistance mediated by its cognate resistance gene Pib, which has been intensively used in indica rice breeding programs in many Asian countries. However, the sequence diversity of AvrPib among geographically distinct M. oryzae populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of AvrPib haplotypes and their pathogenicity against Pib. We found that all of the isolates were virulent to Pib and each of them contained an insertion of Pot3 transposon in AvrPib. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different AvrPib haplotypes, designated avrPib-H1 to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same AvrPib haplotype. In contrast, the isolates having the same AvrPib haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained Pib diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the AvrPib locus and the genome-wide levels, providing insight into the mechanisms of the mutations in AvrPib leading to the breakdown of Pib-mediated resistance in rice.

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