Unraveling NPR-like Family Genes in Fragaria spp. Facilitated to Identify Putative NPR1 and NPR3/4 Orthologues Participating in Strawberry-Colletotrichum fructicola Interaction
<p>The phylogenetic relationships of NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1)-like proteins from <span class="html-italic">Arabidopsis thaliana</span>, five diploid strawberries, and the octoploid strawberry. The tree was clustered into three clades (I, II, and III) shaded with different colors. The length of branches indicates the relative phylogenetic relationship, and the bootstrap values near branches for confidence. Geometries with different shapes and colors are used to symbolize different NPR members, with a star for <span class="html-italic">Arabidopsis</span>, and cycles in red, yellow, green, purple, pink, and gray for <span class="html-italic">Fragaria vesca</span>, <span class="html-italic">F. iinumae</span>, <span class="html-italic">F. viridis</span>, <span class="html-italic">F. nipponica</span>, <span class="html-italic">F. nilgerrensis</span>, and <span class="html-italic">F.</span> × <span class="html-italic">ananassa</span>, respectively.</p> "> Figure 2
<p>The comparative organization of exons and introns in 48 strawberry <span class="html-italic">NPR1</span>-like genes and 6 <span class="html-italic">AtNPRs</span>. The structure was produced with the gene structure display server (GSDS) at <a href="http://gsds.cbi.pku.edu.cn/Chinese.php" target="_blank">http://gsds.cbi.pku.edu.cn/Chinese.php</a> (accessed on 27 February 2022). The blue and the yellow rectangles represent the un-translated regions (UTR) and the coding sequences (CDS), respectively. The neighbor-joining tree of the <span class="html-italic">NPR1</span>-like genes was generated with MUSCLE clustering by MEGA7.0 for CDS nucleotide sequences.</p> "> Figure 3
<p>The comparative protein domain module of six AtNPRs and 48 strawberry NPR1-like sequences. The deduced protein sequences in clade I (<b>A</b>), clade II (<b>B</b>), and clade III (<b>C</b>). The locations of the conserved BTB/POZ domain, the Ankyrin repeats (Ank_2 or Ank_5), and the NPR1/NIM-like defense protein C-terminal region (NPR1_like_C) were revealed via using the web CD Search Tool at NCBI.</p> "> Figure 4
<p>The chromosomal distributions of <span class="html-italic">NPR1</span>-like genes in <span class="html-italic">Fragaria vesca</span> (<b>A</b>) and <span class="html-italic">F.</span> × <span class="html-italic">ananassa</span> (<b>B</b>). The identity of each chromosome (of certain sub-genome) is shown at the top. The scale ruler at the left side indicates the physical distance of chromosomes in megabases (Mb). The location site and the transcriptional direction for each strawberry <span class="html-italic">NPR1</span>-like locus are marked as triangle.</p> "> Figure 5
<p>The predicted cis-elements in the promoter regions of <span class="html-italic">NPR</span>-like genes in <span class="html-italic">Fragaria vesca</span> and <span class="html-italic">F.</span> × <span class="html-italic">ananassa</span>. The promoter sequences (−2500 bp upstream of the starting code ATG) of 48 strawberry <span class="html-italic">NPR</span>-like genes were analyzed by PlantCare. The geometries in different colors and shapes indicate elements involved in different processes, with cycles for hormone-responsive, filled rectangles for stress-responsive, and rectangles with gradient color for the others.</p> "> Figure 6
<p>The expression responses of strawberry <span class="html-italic">NPR</span>-like genes upon <span class="html-italic">Colletotrichum fructicola</span> invasion in diploid ‘Hawaii4’ and octoploid cultivars ‘Camarosa’ and ‘Benihoppe’. (<b>A</b>) The typical symptoms induced by <span class="html-italic">C. fructicola</span> on wounded detached strawberry leaf blades at 25 °C were photographed at 4 and 5 dpi. The left and right side of each leaf blade (adaxial side up) was inoculated with two 10-μL droplets of sterile water with 0.01% (<span class="html-italic">v</span>/<span class="html-italic">v</span>) Tween 20 (Mock, M) and conidia suspension (2 × 10<sup>6</sup> per mL, <span class="html-italic">C. f</span>), respectively. Scale bar, 1 cm. (<b>B</b>) The semi-quantitative RT-PCR analysis of strawberry <span class="html-italic">NPR</span>-like genes. The third, fourth, and fifth compound leaves of sprayed inoculated plants (<span class="html-italic">C. f</span>) or mock-treated (M) were harvested at different hours post inoculation (hpi). The PCR cycle numbers are 40 and 28 for <span class="html-italic">NPR1</span>-likes and the internal control <span class="html-italic">EF1α</span>, respectively. In amplification for <span class="html-italic">FveNPR31</span>, <span class="html-italic">-32a</span>, <span class="html-italic">-32b</span>, and <span class="html-italic">-33</span>, 0.2-μL original cDNAs was used as a template, while for <span class="html-italic">NPR1</span> and <span class="html-italic">-5</span> in both diploid and octoploid strawberry, 1-μL original cDNAs was used.</p> "> Figure 7
<p>A quantitative RT-PCR analysis of strawberry <span class="html-italic">NPR3</span>-like genes upon <span class="html-italic">C. fructicola</span> invasion in diploid ‘Hawaii4’ and octoploid ‘Benihoppe’. The same RNA samples in <a href="#plants-11-01589-f006" class="html-fig">Figure 6</a> were analyzed. The same primer pairs for all <span class="html-italic">NPR3</span>-like genes except for <span class="html-italic">NPR32b</span> were used in <span class="html-italic">F. vesca</span> ‘Hawaii4’ and <span class="html-italic">F.</span> × <span class="html-italic">ananassa</span> ‘Benihoppe’. <span class="html-italic">FvePR10a</span> (FvH4_4g19120) was used as a marker gene of SA-depending defense signaling pathway. The primers and corresponding target alleles amplified were shown in <a href="#app1-plants-11-01589" class="html-app">Supplementary Table S6</a>. The gene name followed with ‘-s’ indicates multiple alleles detected in ‘Benihoppe’. The relative transcript levels of <span class="html-italic">NPR3</span>-like genes were normalized with two reference genes <span class="html-italic">EF1α</span> and <span class="html-italic">GAPDH2</span> [<a href="#B49-plants-11-01589" class="html-bibr">49</a>] and reported as the mean of three biological replicates ± SE. The asterisks indicate significant differences based on a Student <span class="html-italic">t</span>-test analysis (*, <span class="html-italic">p</span> < 0.05).</p> "> Figure 8
<p>The protein–protein interaction networks proposed for the strawberry FveNPR1-like proteins in STRING (<a href="https://cn.string-db.org" target="_blank">https://cn.string-db.org</a>, accessed on 26 February 2022). The edges in different colors represent the predicted interaction relationships according to different methods. The detailed information for all potential partners is shown in <a href="#plants-11-01589-f009" class="html-fig">Figure 9</a> and <a href="#app1-plants-11-01589" class="html-app">Figure S3</a>.</p> "> Figure 9
<p>RNA-seq data showing the differential expression of genes coding proteins potentially directly or indirectly interacting with NPR1-like proteins (<b>A</b>) and the other known members in SA signaling (<b>B</b>) in strawberry during the <span class="html-italic">C. fructicola</span> invasion. The heatmap was generated using RPKM (reads per kilobase per million mapped reads) values normalized via Log2-transformation for each transcript in a moderate susceptible strawberry cv. ‘Jiuxiang’ mock-treated or infected by <span class="html-italic">C. fructicola</span> at 24, 72, or 96 hpi. The black star symbols indicate NPR family members. Strawberry materials and <span class="html-italic">C. fructicola</span> inoculation conditions for RNA-seq data generation have been reported previously [<a href="#B35-plants-11-01589" class="html-bibr">35</a>].</p> "> Figure 10
<p>A hypothetical model depicting the transcriptional events related to NPR1- and NPR31-mediated defenses in susceptible strawberry upon invasion with a hemibiotrophic fungal pathogen <span class="html-italic">Colletotrichum fructicola</span>. (<b>A</b>) At 6 hpi early stage, the strawberry cell accumulates a relatively low or basal level of SA (red cycles). There is no monomeric NPR1 protein (ellipse), and it exists in cytoplasm as a large oligomer or forming heterodimer with the negative regulator NPR31. In the nucleus, the transcription of NPR1 is suppressed, while NPR31 transcription has been restored to a steady state after a transient induction. Simultaneously, the expression of pathogenesis-related gene <span class="html-italic">PR1</span>, as well as SA synthesis genes <span class="html-italic">ICS</span> and <span class="html-italic">PAL</span>, show a similar dynamic pattern to that of <span class="html-italic">NPR31</span>. All events indicate a fast quenching of SA-dependent resistance, resulting in effector (small brown shapes)-triggered susceptibility (ETS). (<b>B</b>) At the 96 hpi late necrotrophic stage, the strawberry cell contains elevated SA due to the increased expression of PAL1/2. SA-dependent resistance is partially activated after NPR1 binds SA. Enhanced NPR31 negatively regulates SA-related immunity. Meanwhile, SA-dependent resistance is antagonized by the disinhibition of MeJA-mediated defense and the activation of ethylene-related defense, which is beneficial for strawberry defending the pathogen with a necrotrophic life at 96 hpi. There exists monomeric NPR1 and NPR31 in the nucleus, which directly target TGA transcriptional factors to regulate the expression of <span class="html-italic">PR</span> genes. Members are in red characters for up-regulated and in blue for down-regulated.</p> "> Figure 10 Cont.
<p>A hypothetical model depicting the transcriptional events related to NPR1- and NPR31-mediated defenses in susceptible strawberry upon invasion with a hemibiotrophic fungal pathogen <span class="html-italic">Colletotrichum fructicola</span>. (<b>A</b>) At 6 hpi early stage, the strawberry cell accumulates a relatively low or basal level of SA (red cycles). There is no monomeric NPR1 protein (ellipse), and it exists in cytoplasm as a large oligomer or forming heterodimer with the negative regulator NPR31. In the nucleus, the transcription of NPR1 is suppressed, while NPR31 transcription has been restored to a steady state after a transient induction. Simultaneously, the expression of pathogenesis-related gene <span class="html-italic">PR1</span>, as well as SA synthesis genes <span class="html-italic">ICS</span> and <span class="html-italic">PAL</span>, show a similar dynamic pattern to that of <span class="html-italic">NPR31</span>. All events indicate a fast quenching of SA-dependent resistance, resulting in effector (small brown shapes)-triggered susceptibility (ETS). (<b>B</b>) At the 96 hpi late necrotrophic stage, the strawberry cell contains elevated SA due to the increased expression of PAL1/2. SA-dependent resistance is partially activated after NPR1 binds SA. Enhanced NPR31 negatively regulates SA-related immunity. Meanwhile, SA-dependent resistance is antagonized by the disinhibition of MeJA-mediated defense and the activation of ethylene-related defense, which is beneficial for strawberry defending the pathogen with a necrotrophic life at 96 hpi. There exists monomeric NPR1 and NPR31 in the nucleus, which directly target TGA transcriptional factors to regulate the expression of <span class="html-italic">PR</span> genes. Members are in red characters for up-regulated and in blue for down-regulated.</p> ">
Abstract
:1. Introduction
2. Results
2.1. Diversity and Phylogeny of NPR-like Members in Fragaria Species
2.2. Structural Features of Fragaria NPR-like Members in DNA and Amino Acid Sequences
2.3. Physical Distribution of NPR1-like Loci in the Genomes of F. vesca and F. × ananassa
2.4. Cis-Elements in the Promoter Regions of NPR-like Genes from F. vesca and F. × ananassa
2.5. Transcriptional Responses of Strawberry NPR-like Genes to C. fructicola
2.6. Transcriptome Profile of NPR-like and Related Genes in Strawberry Infected with C. fructicola
3. Discussion
4. Materials and Methods
4.1. Plant Materials, Growth Conditions, and Inoculation with C. fructicola
4.2. Identification and Phylogenic Analysis of NPR-like Genes in Fragaria Species
4.3. Exon-Intron Structure in NPR-like Genes and Domain Organization in Deduced Proteins
4.4. Chromosomal Locations of NPR-like Genes in F. vesca and F. × ananassa
4.5. Cis-Elements in Promoters of NPR-like Loci in F. vesca and F. × ananassa
4.6. Protein-Protein Interaction Prediction for Strawberry NPR-like Proteins
4.7. RNA Purification, RT-PCR, and RNA Sequencing
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Cao, H.; Bowling, S.A.; Gordon, A.S.; Dong, X. Characterization of an Arabidopsis Mutant That Is Nonresponsive to Inducers of Systemic Acquired Resistance. Plant Cell 1994, 6, 1583–1592. [Google Scholar] [CrossRef] [PubMed]
- Kinkema, M.; Fan, W.; Dong, X. Nuclear localization of NPR1 is required for activation of PR gene expression. Plant Cell 2000, 12, 2339–2350. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mou, Z.; Fan, W.; Dong, X. Inducers of plant systemic acquired resistance regulate NPR1 function through redox changes. Cell 2003, 113, 935–944. [Google Scholar] [CrossRef] [Green Version]
- Fu, Z.Q.; Yan, S.; Saleh, A.; Wang, W.; Ruble, J.; Oka, N.; Mohan, R.; Spoel, S.H.; Tada, Y.; Zheng, N.; et al. NPR3 and NPR4 are receptors for the immune signal salicylic acid in plants. Nature 2012, 486, 228–232. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Saleh, A.; Withers, J.; Mohan, R.; Marqués, J.; Gu, Y.; Yan, S.; Zavaliev, R.; Nomoto, M.; Tada, Y.; Dong, X. Posttranslational Modifications of the Master Transcriptional Regulator NPR1 Enable Dynamic but Tight Control of Plant Immune Responses. Cell Host Microbe 2015, 18, 169–182. [Google Scholar] [CrossRef] [Green Version]
- Liu, Y.; Sun, T.; Sun, Y.; Zhang, Y.; Radojičić, A.; Ding, Y.; Tian, H.; Huang, X.; Lan, J.; Chen, S.; et al. Diverse Roles of the Salicylic Acid Receptors NPR1 and NPR3/NPR4 in Plant Immunity. Plant Cell 2020, 32, 4002–4016. [Google Scholar] [CrossRef]
- Ding, P.; Ding, Y. Stories of Salicylic Acid: A Plant Defense Hormone. Trends Plant Sci. 2020, 25, 549–565. [Google Scholar] [CrossRef]
- Paeng, S.K.; Chi, Y.H.; Kang, C.H.; Chae, H.B.; Lee, E.S.; Park, J.H.; Wi, S.D.; Bae, S.B.; Phan, K.A.T.; Lee, S.Y. Chaperone function of Arabidopsis NPR1. Plant Biotechnol. Rep. 2020, 14, 227–233. [Google Scholar] [CrossRef]
- Wang, W.; Withers, J.; Li, H.; Zwack, P.J.; Rusnac, D.V.; Shi, H.; Liu, L.; Yan, S.; Hinds, T.R.; Guttman, M.; et al. Structural basis of salicylic acid perception by Arabidopsis NPR proteins. Nature 2020, 586, 311–316. [Google Scholar] [CrossRef]
- Zhang, Y.; Cheng, Y.T.; Qu, N.; Zhao, Q.; Bi, D.; Li, X. Negative regulation of defense responses in Arabidopsis by two NPR1 paralogs. Plant J. 2006, 48, 647–656. [Google Scholar] [CrossRef]
- Endah, R.; Beyene, G.; Kiggundu, A.; van den Berg, N.; Schluter, U.; Kunert, K.; Chikwamba, R. Elicitor and Fusarium-induced expression of NPR1-like genes in banana. Plant Physiol. Biochem. 2008, 46, 1007–1014. [Google Scholar] [CrossRef]
- Bergeault, K.; Bertsch, C.; Merdinoglu, D.; Walter, B. Low level of polymorphism in two putative NPR1 homologs in the Vitaceae family. Biol. Direct 2010, 5, 9. [Google Scholar] [CrossRef] [Green Version]
- Backer, R.; Mahomed, W.; Reeksting, B.J.; Engelbrecht, J.; Ibarra-Laclette, E.; van den Berg, N. Phylogenetic and expression analysis of the NPR1-like gene family from Persea americana (Mill.). Front. Plant. Sci. 2015, 6, 300. [Google Scholar] [CrossRef] [Green Version]
- Shu, L.J.; Liao, J.Y.; Lin, N.C.; Chung, C.L. Identification of a strawberry NPR-like gene involved in negative regulation of the salicylic acid-mediated defense pathway. PLoS ONE 2018, 13, e0205790. [Google Scholar] [CrossRef]
- Liu, X.; Liu, Z.; Niu, X.; Xu, Q.; Yang, L. Genome-Wide Identification and Analysis of the NPR1-Like Gene Family in Bread Wheat and Its Relatives. Int. J. Mol. Sci. 2019, 20, 5974. [Google Scholar] [CrossRef] [Green Version]
- Agarwal, N.; Srivastava, R.; Verma, A.; Rai, K.M.; Singh, B.; Verma, P.C. Unravelling Cotton Nonexpressor of Pathogenesis-Related 1(NPR1)-Like Genes Family: Evolutionary Analysis and Putative Role in Fiber Development and Defense Pathway. Plants 2020, 9, 999. [Google Scholar] [CrossRef]
- Chen, Q.; Wang, L.; Liu, D.; Ma, S.; Dai, Y.; Zhang, X.; Wang, Y.; Hu, T.; Xiao, M.; Zhou, Y.; et al. Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum. Plants 2020, 9, 1448. [Google Scholar] [CrossRef]
- Li, R.; Li, Y.; Zhang, Y.; Sheng, J.; Zhu, H.; Shen, L. Transcriptome analysis reveals that SlNPR1 mediates tomato fruit resistance against Botrytis cinerea by modulating phenylpropanoid metabolism and balancing ROS homeostasis. Postharvest Biol. Technol. 2021, 172, 111382. [Google Scholar] [CrossRef]
- Wang, P.; Zhao, Z.; Zhang, Z.; Cai, Z.; Liao, J.; Tan, Q.; Xiang, M.; Chang, L.; Xu, D.; Tian, Q.; et al. Genome-wide identification and analysis of NPR family genes in Brassica juncea var. tumida. Gene 2021, 769, 145210. [Google Scholar] [CrossRef]
- Wei, Y.; Zhao, S.; Liu, N.; Zhang, Y. Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears. PeerJ 2021, 9, e12617. [Google Scholar] [CrossRef]
- Backer, R.; Naidoo, S.; van den Berg, N. The NONEXPRESSOR of PATHOGENESIS-RELATED GENES 1 (NPR1) and RELATED FAMILY: Mechanistic insights in plant disease resistance. Front. Plant Sci. 2019, 10, 102. [Google Scholar] [CrossRef] [Green Version]
- Darrow, G.M. The Strawberry History, Breeding and Physiology; Mickey, G.H., Ed.; Holt, Rinehart and Winston: New York, NY, USA, 1966. [Google Scholar]
- Edger, P.P.; Poorten, T.J.; VanBuren, R.; Hardigan, M.A.; Colle, M.; McKain, M.R.; Smith, R.D.; Teresi, S.J.; Nelson, A.D.L.; Wai, C.M.; et al. Origin and evolution of the octoploid strawberry genome. Nat. Genet. 2019, 51, 541–547. [Google Scholar] [CrossRef] [Green Version]
- Li, G.; Wang, H.; Cheng, X.; Su, X.; Zhao, Y.; Jiang, T.; Jin, Q.; Lin, Y.; Cai, Y. Comparative genomic analysis of the PAL genes in five Rosaceae species and functional identification of Chinese white pear. PeerJ 2019, 7, e8064. [Google Scholar] [CrossRef] [Green Version]
- Liu, T.; Li, M.; Liu, Z.; Ai, X.; Li, Y. Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. Hortic. Res. 2021, 8, 41. [Google Scholar] [CrossRef]
- Qiao, Q.; Edger, P.P.; Xue, L.; Qiong, L.; Lu, J.; Zhang, Y.; Cao, Q.; Yocca, A.E.; Platts, A.E.; Knapp, S.J.; et al. Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). Proc. Natl. Acad. Sci. USA 2021, 118, e2105431118. [Google Scholar] [CrossRef]
- Liston, A.; Wei, N.; Tennessen, J.A.; Li, J.; Dong, M.; Ashman, T.-L. Revisiting the origin of octoploid strawberry. Nat. Genet. 2020, 52, 2–4. [Google Scholar] [CrossRef]
- Feng, C.; Wang, J.; Harris, A.J.; Folta, K.M.; Zhao, M.; Kang, M. Tracing the Diploid Ancestry of the Cultivated Octoploid Strawberry. Mol. Biol. Evol. 2021, 38, 478–485. [Google Scholar] [CrossRef]
- Hardigan, M.A.; Lorant, A.; Pincot, D.D.A.; Feldmann, M.J.; Famula, R.A.; Acharya, C.B.; Lee, S.; Verma, S.; Whitaker, V.M.; Bassil, N.; et al. Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry. Mol. Biol. Evol. 2021, 38, 2285–2305. [Google Scholar] [CrossRef]
- Wang, L.; Guo, Z.; Zhang, Y.; Wang, Y.; Yang, G.; Yang, L.; Wang, L.; Wang, R.; Xie, Z. Overexpression of LhSorNPR1, a NPR1-like gene from the oriental hybrid lily ‘Sorbonne’, conferred enhanced resistance to Pseudomonas syringae pv. tomato DC3000 in Arabidopsis. Physiol. Mol. Biol. Plants 2017, 23, 793–808. [Google Scholar] [CrossRef]
- Wang, Z.; Zhang, W.-H.; Ma, L.-Y.; Li, X.; Zhao, F.-Y.; Tan, X.-L. Overexpression of Brassica napus NPR1 enhances resistance to Sclerotinia sclerotiorum in oilseed rape. Physiol. Mol. Plant Pathol. 2020, 110, 101460. [Google Scholar] [CrossRef]
- Peng, A.; Zou, X.; He, Y.; Chen, S.; Liu, X.; Zhang, J.; Zhang, Q.; Xie, Z.; Long, J.; Zhao, X. Overexpressing a NPR1-like gene from Citrus paradisi enhanced Huanglongbing resistance in C. sinensis. Plant Cell Rep. 2021, 40, 529–541. [Google Scholar] [CrossRef] [PubMed]
- Silva, K.J.P.; Brunings, A.; Peres, N.A.; Mou, Z.; Folta, K.M. The Arabidopsis NPR1 gene confers broad-spectrum disease resistance in strawberry. Transgenic Res. 2015, 24, 693–704. [Google Scholar] [CrossRef] [PubMed]
- Amil-Ruiz, F.; Garrido-Gala, J.; Gadea, J.; Blanco-Portales, R.; Muñoz-Mérida, A.; Trelles, O.; de Los Santos, B.; Arroyo, F.T.; Aguado-Puig, A.; Romero, F.; et al. Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction. Front. Plant Sci. 2016, 7, 1036. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhang, L.; Huang, X.; He, C.; Zhang, Q.Y.; Zou, X.; Duan, K.; Gao, Q. Novel Fungal Pathogenicity and Leaf Defense Strategies Are Revealed by Simultaneous Transcriptome Analysis of Colletotrichum fructicola and Strawberry Infected by This Fungus. Front Plant Sci. 2018, 9, 434. [Google Scholar] [CrossRef] [Green Version]
- He, C.; Duan, K.; Zhang, L.; Zhang, L.; Song, L.; Yang, J.; Zou, X.; Wang, Y.; Gao, Q. Fast Quenching the Burst of Host Salicylic Acid Is Common in Early Strawberry/Colletotrichum fructicola Interaction. Phytopathology 2019, 109, 531–541. [Google Scholar] [CrossRef] [Green Version]
- Feng, J.; Cheng, Y.; Zheng, C. Expression patterns of octoploid strawberry TGA genes reveal a potential role in response to Podosphaera aphanis infection. Plant Biotechnol. Rep. 2019, 14, 55–67. [Google Scholar] [CrossRef]
- Feng, J.; Zhang, M.; Yang, K.N.; Zheng, C.X. Salicylic acid-primed defence response in octoploid strawberry ‘Benihoppe’ leaves induces resistance against Podosphaera aphanis through enhanced accumulation of proanthocyanidins and upregulation of pathogenesis-related genes. BMC Plant Biol. 2020, 20, 149. [Google Scholar] [CrossRef] [Green Version]
- Maier, F.; Zwicker, S.; Huckelhoven, A.; Meissner, M.; Funk, J.; Pfitzner, A.J.; Pfitzner, U.M. nonexpressor of pathogenesis-related proteins1 (NPR1) and some NPR1-related proteins are sensitive to salicylic acid. Mol. Plant Pathol. 2011, 12, 73–91. [Google Scholar] [CrossRef]
- Germain, H.; Lachance, D.; Pelletier, G.; Fossdal, C.G.; Solheim, H.; Séguin, A. The expression pattern of the Picea glauca Defensin 1 promoter is maintained in Arabidopsis thaliana, indicating the conservation of signalling pathways between angiosperms and gymnosperms. J. Exp. Bot. 2012, 63, 785–795. [Google Scholar] [CrossRef] [Green Version]
- Chen, C.; Chen, Z. Potentiation of developmentally regulated plant defense response by AtWRKY18, a pathogen-induced Arabidopsis transcription factor. Plant Physiol. 2002, 129, 706–716. [Google Scholar] [CrossRef] [Green Version]
- Xu, X.; Chen, C.; Fan, B.; Chen, Z. Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors. Plant Cell 2006, 18, 1310–1326. [Google Scholar] [CrossRef] [Green Version]
- Goldsbrough, A.P.; Albrecht, H.; Stratford, R. Salicylic acid-inducible binding of a tobacco nuclear protein to a 10 bp sequence which is highly conserved amongst stress-inducible genes. Plant J. 1993, 3, 563–571. [Google Scholar] [CrossRef]
- Salazar, M.; González, E.; Casaretto, J.A.; Casacuberta, J.M.; Ruiz-Lara, S. The promoter of the TLC1.1 retrotransposon from Solanum chilense is activated by multiple stress-related signaling molecules. Plant Cell Rep. 2007, 26, 1861–1868. [Google Scholar] [CrossRef]
- Ulmasov, T.; Hagen, G.; Guilfoyle, T. The ocs element in the soybean GH2/4 promoter is activated by both active and inactive auxin and salicylic acid analogues. Plant Mol. Biol. 1994, 26, 1055–1064. [Google Scholar] [CrossRef]
- Xiang, C.; Miao, Z.H.; Lam, E. Coordinated activation of as-1-type elements and a tobacco glutathione S-transferase gene by auxins, salicylic acid, methyl-jasmonate and hydrogen peroxide. Plant Mol. Biol. 1996, 32, 415–426. [Google Scholar] [CrossRef]
- Krawczyk, S.; Thurow, C.; Niggeweg, R.; Gatz, C. Analysis of the spacing between the two palindromes of activation sequence-1 with respect to binding to different TGA factors and transcriptional activation potential. Nucleic Acids Res. 2002, 30, 775–781. [Google Scholar] [CrossRef] [Green Version]
- Chen, J.; Zhang, J.; Kong, M.; Freeman, A.; Chen, H.; Liu, F. More stories to tell: NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1, a salicylic acid receptor. Plant Cell Environ. 2021, 44, 1716–1727. [Google Scholar] [CrossRef]
- Amil-Ruiz, F.; Garrido-Gala, J.; Blanco-Portales, R.; Folta, K.M.; Muñoz-Blanco, J.; Caballero, J.L. Identification and validation of reference genes for transcript normalization in strawberry (Fragaria × ananassa) defense responses. PLoS ONE 2013, 8, e70603. [Google Scholar] [CrossRef] [Green Version]
- Liu, G.; Holub, E.B.; Alonso, J.M.; Ecker, J.R.; Fobert, P.R. An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. Plant J. 2005, 41, 304–318. [Google Scholar] [CrossRef]
- Yuan, Y.; Zhong, S.; Li, Q.; Zhu, Z.; Lou, Y.; Wang, L.; Wang, J.; Wang, M.; Li, Q.; Yang, D.; et al. Functional analysis of rice NPR1-like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility. Plant Biotechnol. J. 2007, 5, 313–324. [Google Scholar] [CrossRef]
- Wang, Z.; Ma, L.Y.; Li, X.; Zhao, F.Y.; Sarwar, R.; Cao, J.; Li, Y.L.; Ding, L.N.; Zhu, K.M.; Yang, Y.H.; et al. Genome-wide identification of the NPR1-like gene family in Brassica napus and functional characterization of BnaNPR1 in resistance to Sclerotinia sclerotiorum. Plant Cell Rep. 2020, 39, 709–722. [Google Scholar] [CrossRef]
- Amil-Ruiz, F. Molecular Mechanisms of Strawberry Plant Defence against Colletotrichum acutatum. Ph.D. Thesis, Universidad de Córdoba, Córdoba, Spain, 2013. [Google Scholar]
- Tada, Y.; Spoel, S.H.; Pajerowska-Mukhtar, K.; Mou, Z.; Song, J.; Wang, C.; Zuo, J.; Dong, X. Plant immunity requires conformational changes of NPR1 via S-nitrosylation and thioredoxins. Science 2008, 321, 952–956. [Google Scholar] [CrossRef] [Green Version]
- Ding, Y.; Sun, T.; Ao, K.; Peng, Y.; Zhang, Y.; Li, X.; Zhang, Y. Opposite Roles of Salicylic Acid Receptors NPR1 and NPR3/NPR4 in Transcriptional Regulation of Plant Immunity. Cell 2018, 173, 1454–1467.e15. [Google Scholar] [CrossRef]
- Ha, C.M.; Jun, J.H.; Nam, H.G.; Fletcher, J.C. BLADE-ON-PETIOLE1 Encodes a BTB/POZ Domain Protein Required for Leaf Morphogenesis in Arabidopsis thaliana. Plant Cell Physiol. 2004, 45, 1361–1370. [Google Scholar] [CrossRef]
- Wang, Y.; Salasini, B.C.; Khan, M.; Devi, B.; Bush, M.; Subramaniam, R.; Hepworth, S.R. Clade I TGACG-Motif Binding Basic Leucine Zipper Transcription Factors Mediate BLADE-ON-PETIOLE-Dependent Regulation of Development. Plant Physiol. 2019, 180, 937–951. [Google Scholar] [CrossRef] [Green Version]
- Peng, Y.; Yang, J.; Li, X.; Zhang, Y. Salicylic Acid: Biosynthesis and Signaling. Annu. Rev. Plant Biol. 2021, 72, 761–791. [Google Scholar] [CrossRef]
- Kang, C.; Darwish, O.; Geretz, A.; Shahan, R.; Alkharouf, N.; Liu, Z. Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. Plant Cell 2013, 25, 1960–1978. [Google Scholar] [CrossRef] [Green Version]
- Xu, G.; Yuan, M.; Ai, C.; Liu, L.; Zhuang, E.; Karapetyan, S.; Wang, S.; Dong, X. uORF-mediated translation allows engineered plant disease resistance without fitness costs. Nature 2017, 545, 491–494. [Google Scholar] [CrossRef]
- Ren, X.; Li, Y.; Lu, J.; Yang, B.; Dai, F. Identification of Colletotrichum species from strawberry in Shanghai. Acta Phytopathol. Sin. 2008, 3, 325–328. (In Chinese) [Google Scholar]
- Chung, P.C.; Wu, H.Y.; Wang, Y.W.; Ariyawansa, H.A.; Hu, H.P.; Hung, T.H.; Tzean, S.S.; Chung, C.L. Diversity and pathogenicity of Colletotrichum species causing strawberry anthracnose in Taiwan and description of a new species, Colletotrichum miaoliense sp. nov. Sci. Rep. 2020, 10, 14664. [Google Scholar] [CrossRef]
- Jung, S.; Lee, T.; Cheng, C.-H.; Buble, K.; Zheng, P.; Yu, J.; Humann, J.; Ficklin, S.P.; Gasic, K.; Scott, K.; et al. 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Res. 2019, 47, D1137–D1145. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 2016, 33, 1870–1874. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Letunic, I.; Bork, P. Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016, 44, W242–W245. [Google Scholar] [CrossRef] [PubMed]
- Liu, W.; Xie, Y.; Ma, J.; Luo, X.; Nie, P.; Zuo, Z.; Lahrmann, U.; Zhao, Q.; Zheng, Y.; Zhao, Y.; et al. IBS: An illustrator for the presentation and visualization of biological sequences. Bioinformatics 2015, 31, 3359–3361. [Google Scholar] [CrossRef] [Green Version]
- Waterhouse, A.M.; Procter, J.B.; Martin, D.M.A.; Clamp, M.; Barton, G.J. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25, 1189–1191. [Google Scholar] [CrossRef] [Green Version]
- Voorrips, R.E. MapChart: Software for the graphical presentation of linkage maps and QTLs. J. Hered. 2002, 93, 77–78. [Google Scholar] [CrossRef] [Green Version]
- Lescot, M.; Déhais, P.; Thijs, G.; Marchal, K.; Moreau, Y.; Van de Peer, Y.; Rouzé, P.; Rombauts, S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30, 325–327. [Google Scholar] [CrossRef]
- Chen, C.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.; Xia, R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol. Plant. 2020, 13, 1194–1202. [Google Scholar] [CrossRef]
- Szklarczyk, D.; Gable, A.L.; Nastou, K.C.; Lyon, D.; Kirsch, R.; Pyysalo, S.; Doncheva, N.T.; Legeay, M.; Fang, T.; Bork, P.; et al. The STRING database in 2021: Customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 2021, 49, D605–D612. [Google Scholar] [CrossRef]
- Vandesompele, J.; De Preter, K.; Pattyn, F.; Poppe, B.; Van Roy, N.; De Paepe, A.; Speleman, F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3, 1–2. [Google Scholar] [CrossRef] [Green Version]
GENE NAME | Locus ID | Chromosomal Location | DNA (bp) | mRNA (bp) | Protein (aa) | LOC a | MW b (kDa) | Pi c |
---|---|---|---|---|---|---|---|---|
FnilNPR1 | FnYN1G009790 | GWHABKC00000007:1g6682576-6684604 | 2029 | 1758 | 585 | Nuc:Ct_Nuc (6.5:6) | 64.7 | 6.74 |
FnilNPR31 | FnYN3G011400 | GWHABKC00000002:3g8012487-8017100 | 4614 | 3096 | 587 | Ct:ER (4:3) | 65.3 | 6.39 |
FnilNPR32 | FnYN6G037850 | GWHABKC00000001:6g39083311-39088355 | 5045 | 2958 | 592 | Ct | 66.3 | 5.87 |
FnilNPR33 | FnYN6G037830 | GWHABKC00000001:6g39072614-39077826 | 5213 | 2660 | 578 | Nuc | 64.7 | 5.77 |
FnilNPR5 | FnYN6G024190 | GWHABKC00000001:6g24090462-24093763 | 3302 | 2430 | 506 | CL:ER(4:3) | 55.1 | 6.30 |
FiinNPR1 | evm.model.scaf_79.680 | Chr1:3535351-3537414 | 2064 | 1749 | 582 | Ct:Ct_Nuc (6.5:6.5) | 64.6 | 6.34 |
FiinNPR31 | evm.model.scaf_86.217 | Chr3:6321505-6326064 | 4560 | 3037 | 587 | CL:Ct:ER(3:3:3) | 65.3 | 6.15 |
FiinNPR32 | evm.model.scaf_41.1197 | Chr6:34174583-34181716 | 7134 | 5053 | 592 | Nuc | 66.1 | 5.88 |
FiinNPR33 | evm.model.scaf_41.1198 | Chr6:34168193-34173663 | 5471 | 2786 | 578 | Nuc | 64.8 | 5.71 |
FiinNPR5 | evm.model.scaf_63.37 | Chr6:22982676-22985547 | 2872 | 1994 | 506 | CL:ER(4:3) | 55.2 | 6.25 |
FnipNPR31 | FNI_iscf00049273 | FNI_iscf00049273.1:1606-6149 | 4544 | 3026 | 586 | CL:Ct:ER(3:3:3) | 65.2 | 6.48 |
FnipNPR33 | FNI_icon04446061 | FNI_icon04446061.1:1..1551 | 1551 | 1244 | 331 | CL:Ct (5:4) | 37.5 | 5.93 |
FnipNPR5 | FNI_icon04380981 | FNI_icon04380981.1:1-919 | 919 | 919 | 190 | Ct | 21.3 | 5.44 |
FvirNPR1 | evm.model.ctg104.806 | Fvir1_FvScbg_v1.0:4416036-4423359 | 7324 | 1830 | 579 | Nuc:Ct_Nuc (6.5:6) | 64.2 | 6.39 |
FvirNPR31 | evm.model.ctg53.483 | Fvir3_FvScbg_v1.0:7054130-7058288 | 4159 | 2628 | 587 | CL:Ct:ER(3:3:3) | 65.3 | 6.46 |
FvirNPR32a | evm.model.ctg16.266 | Fvir6_FvScbg_v1.0:28680195-28684954 | 4760 | 2667 | 592 | Ct | 66.3 | 5.84 |
FvirNPR32b | evm.model.ctg16.265 | Fvir6_FvScbg_v1.0:28677873-28679626 | 1754 | 978 | 172 | Nuc:Nuc_Pm (7: 5.5) | 19.3 | 5.47 |
FvirNPR33 | evm.model.ctg16.264 | Fvir6_FvScbg_v1.0:28671131-28675723 | 4593 | 2056 | 578 | Nuc | 64.7 | 5.71 |
FvirNPR5 | evm.model.ctg10.1018 | Fvir6_FvScbg_v1.0:17711496-17714838 | 3343 | 2466 | 506 | CL:ER(4:3) | 55.1 | 6.30 |
FveNPR1 | FvH4_1g07810 | Fvb1_v4.0.a1:1g4137661-4139975 | 2315 | 2001 | 595 | Ct_Nuc:Nuc:Ct (5:4.5:4.5) | 66.1 | 6.56 |
FveNPR31 | FvH4_3g11950 | Fvb3_v4.0.a1:3g7057867-7062282 | 4763 | 3137 | 559 | Nuc:Ct_Nuc (6.5:5.5) | 62.5 | 6.62 |
FveNPR32a | FvH4_6g38830 | Fvb6_v4.0.a1:6g30715984-30720865 | 5163 | 3125 | 591 | Nuc | 65.9 | 6.21 |
FveNPR32b | FvH4_6g38821 | Fvb6_v4.0.a1:6g30713812-30715119 | 1308 | 510 | 169 | Ct | 18.9 | 6.52 |
FveNPR33 | FvH4_6g38820 | Fvb6_v4.0.a1:6g30706741-30711990 | 5250 | 2720 | 578 | Nuc | 64.6 | 5.77 |
FveNPR5 | FvH4_6g25090 | Fvb6_v4.0.a1:6g19041447-19045465 | 4019 | 3135 | 506 | CL:ER(4:3) | 55.1 | 6.30 |
FxaNPR1a | FxaC_1g08070 | Fvb1-4:1g3379833-3381904 | 2072 | 1758 | 585 | Nuc:Ct_Nuc (6.5:6.5) | 65.0 | 6.31 |
FxaNPR1b | FxaC_3g07950 | Fvb1-3:3g3702237-3704301 | 2065 | 1758 | 585 | Nuc:Ct_Nuc:Ct (6.5:6.5:5.5) | 64.8 | 6.34 |
FxaNPR1c | FxaC_2g04070 | Fvb1-2:2g1987750-1989813 | 2064 | 1758 | 585 | Nuc:Ct_Nuc:Ct (6.5:6.5:5.5) | 64.8 | 6.31 |
FxaNPR1d | FxaC_2g12680 | Fvb1-2:2g5651753-5653817 | 2065 | 1758 | 585 | Nuc:Ct_Nuc:Ct (6.5:6.5:5.5) | 64.9 | 6.74 |
FxaNPR1e | FxaC_4g32730 | Fvb1-1:4g24082443-24086784 | 4342 | 1443 | 480 | CL:Ct_Nuc(6:4.5) | 53.1 | 6.17 |
FxaNPR31a | FxaC_12g38540 | Fvb3-1:12g25671777-25676553 | 4777 | 3253 | 587 | CL:Ct:Vc(3:3:3) | 65.4 | 6.69 |
FxaNPR31b | FxaC_11g10120 | Fvb3-3:11g4779868-4784455 | 4588 | 3087 | 587 | Ct:Nuc(4:3) | 65.3 | 6.39 |
FxaNPR31c | FxaC_10g12880 | Fvb3-2:10g6319585-6324148 | 4564 | 3026 | 587 | CL:Ct:ER(3:3:3) | 65.2 | 6.33 |
FxaNPR32a | FxaC_22g16240 | Fvb6-3:22g7985231-7990237 | 5007 | 2939 | 592 | Nuc | 66.1 | 6.10 |
FxaNPR32b | FxaC_21g19040 | Fvb6-1:21g8680678-8685655 | 4978 | 2943 | 591 | Nuc | 65.9 | 6.24 |
FxaNPR32c | FxaC_24g47651 | Fvb6-4:24g28858157-28862733 | 4577 | 2505 | 592 | Ct | 66.1 | 6.07 |
FxaNPR32d | FxaC_23g61170 | Fvb6-2:23g35711876-35716520 | 4645 | 2552 | 592 | Ct | 66.3 | 6.94 |
FxaNPR32e | FxaC_22g16241 | Fvb6-3:22g7990555-7992532 | 1978 | 1213 | 163 | Nuc:Nuc_Pm(6:5) | 18.0 | 6.31 |
FxaNPR32f | FxaC_24g47650 | Fvb6-4:24g28855998-28856575 | 578 | 318 | 105 | CL | 12.1 | 5.29 |
FxaNPR32g | FxaC_21g19041 | Fvb6-1:21g8686054-8687896 | 1843 | 1051 | 169 | Ct | 18.8 | 6.21 |
FxaNPR33a | FxaC_21g19050 | Fvb6-1:21g8689400-8694727 | 5328 | 2804 | 578 | Nuc | 64.6 | 5.83 |
FxaNPR33b | FxaC_23g61160 | Fvb6-2:23g35703222-35708378 | 5157 | 2657 | 578 | Nuc | 64.7 | 5.71 |
FxaNPR33c | FxaC_22g16250 | Fvb6-3:22g7993972-7999331 | 5360 | 2868 | 578 | Nuc | 64.8 | 5.77 |
FxaNPR33d | FxaC_24g47640 | Fvb6-4:24g28849358-28854622 | 5265 | 2733 | 578 | Nuc | 64.9 | 5.55 |
FxaNPR5a | FxaC_21g36330 | Fvb6-1:21g18274937-18277824 | 2888 | 2040 | 506 | CL:ER(4:3) | 55.1 | 6.28 |
FxaNPR5b | FxaC_22g32930 | Fvb6-3:22g19234481-19237536 | 3056 | 2197 | 506 | CL:ER(4:3) | 55.3 | 6.27 |
FxaNPR5c | FxaC_23g15430 | Fvb6-2:23g10470309-10473618 | 3310 | 2467 | 506 | CL:ER(4:3) | 55.2 | 6.20 |
FxaNPR5d | FxaC_24g32090 | Fvb6-4:24g18449601-18452673 | 3073 | 2192 | 502 | CL:ER(4:3) | 54.7 | 6.23 |
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Bai, Y.; Li, Z.; Zhu, J.; Chen, S.; Dong, C.; Gao, Q.; Duan, K. Unraveling NPR-like Family Genes in Fragaria spp. Facilitated to Identify Putative NPR1 and NPR3/4 Orthologues Participating in Strawberry-Colletotrichum fructicola Interaction. Plants 2022, 11, 1589. https://doi.org/10.3390/plants11121589
Bai Y, Li Z, Zhu J, Chen S, Dong C, Gao Q, Duan K. Unraveling NPR-like Family Genes in Fragaria spp. Facilitated to Identify Putative NPR1 and NPR3/4 Orthologues Participating in Strawberry-Colletotrichum fructicola Interaction. Plants. 2022; 11(12):1589. https://doi.org/10.3390/plants11121589
Chicago/Turabian StyleBai, Yun, Ziyi Li, Jiajun Zhu, Siyu Chen, Chao Dong, Qinghua Gao, and Ke Duan. 2022. "Unraveling NPR-like Family Genes in Fragaria spp. Facilitated to Identify Putative NPR1 and NPR3/4 Orthologues Participating in Strawberry-Colletotrichum fructicola Interaction" Plants 11, no. 12: 1589. https://doi.org/10.3390/plants11121589