1
|
Augustine L, Varghese L, Kappachery S, Ramaswami VM, Surendrababu SP, Sakuntala M, Thomas G. Comparative analyses reveal a phenylalanine ammonia lyase dependent and salicylic acid mediated host resistance in Zingiber zerumbet against the necrotrophic soft rot pathogen Pythium myriotylum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111972. [PMID: 38176527 DOI: 10.1016/j.plantsci.2023.111972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
Little is known about the molecular basis of host defense in resistant wild species Zingiber zerumbet (L.) Smith against the soil-borne, necrotrophic oomycete pathogen Pythium myriotylum Drechsler, which causes the devastating soft rot disease in the spice crop ginger (Zingiber officinale Roscoe). We investigated the pattern of host defense between Z. zerumbet and ginger in response to P. myriotylum inoculation. Analysis of gene expression microarray data revealed enrichment of phenylpropanoid biosynthetic genes, particularly lignin biosynthesis genes, in pathogen-inoculated Z. zerumbet compared to ginger. RT-qPCR analysis showed the robust activation of phenylpropanoid biosynthesis genes in Z. zerumbet, including the core genes PAL, C4H, 4CL, and the monolignol biosynthesis and polymerization genes such as CCR, CAD, C3H, CCoAOMT, F5H, COMT, and LAC. Additionally, Z. zerumbet exhibited the accumulation of the phenolic acids including p-coumaric acid, sinapic acid, and ferulic acid that are characteristic of the cell walls of commelinoid monocots like Zingiberaceae and are involved in cell wall strengthening by cross linking with lignin. Z. zerumbet also had higher total lignin and total phenolics content compared to pathogen-inoculated ginger. Phloroglucinol staining revealed the enhanced fortification of cell walls in Z. zerumbet, specifically in xylem vessels and surrounding cells. The trypan blue staining indicated inhibition of pathogen growth in Z. zerumbet at the first leaf whorl, while ginger showed complete colonization of the pith within 36 h post inoculation (hpi). Accumulation of salicylic acid (SA) and induction of SA regulator NPR1 and the signaling marker PR1 were observed in Z. zerumbet. Silencing of PAL in Z. zerumbet through VIGS suppressed downstream genes, leading to reduced phenylpropanoid accumulation and SA level, resulting in the susceptibility of plants to P. myriotylum. These findings highlight the essential role of PAL-dependent mechanisms in resistance against P. myriotylum in Z. zerumbet. Moreover, our results suggest an unconventional role for SA in mediating host resistance against a necrotroph. Targeting the phenylpropanoid pathway could be a promising strategy for the effective management of P. myriotylum in ginger.
Collapse
Affiliation(s)
- Lesly Augustine
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India; Research Centre, University of Kerala, Thiruvananthapuram 695034, India
| | - Lini Varghese
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India; Research Centre, University of Kerala, Thiruvananthapuram 695034, India
| | - Sajeesh Kappachery
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India; Research Centre, University of Kerala, Thiruvananthapuram 695034, India
| | - Vinitha Meenakshy Ramaswami
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
| | - Swathy Puthanvila Surendrababu
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India; Research Centre, University of Kerala, Thiruvananthapuram 695034, India.
| | - Manjula Sakuntala
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India
| | - George Thomas
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, Kerala, India.
| |
Collapse
|
2
|
Narayanrao DR, Tomar RS, Sm P, Jasminkumar K, Ashish G, Chauhan NM, Singh SC, Upadhye V, Kuddus M, Kamble L, Hajare ST. De novo transcriptome sequencing of drought tolerance-associated genes in little millet (Panicum sumatrense L.). Funct Integr Genomics 2023; 23:303. [PMID: 37723408 DOI: 10.1007/s10142-023-01221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/20/2023]
Abstract
The genome size of the little millet Panicum sumatrense is unknown, although its genome is fairly diploid (2n = 4x = 36). Despite tremendous nutritional value and adaptability to adverse climatic conditions, P. sumatrense use was limited by their low palatability, coarse grain, and lack of variety of culinary preparations. Hence, understanding how to vary their usage to offer food and nutritional security in the continuously changing modern world, the proposed study was aimed to determine potential genes and metabolites implicated in drought resistance. The drought-resistant genotype of tiny millet OLM-203/Tarini was offered in pots under both relaxed and demanding circumstances. The experimental seedlings were 32 days old and had been under water stress for 23 days. A total of 7606 genes were compared between 23 and 32 days for roots and 7264 total genes were compared between 23 and 32 days for leaves, according to a research on differential expression genes (DEGs). Twenty essential genes for drought tolerance were up-or down-regulated in the control and treated roots of the OLM-203 genotype. For instance, the genes RS193 and XB34 were up-regulated in leaves while, WLIM1 was found to be down-regulated. Gene SKI35 was up-regulated in roots, whereas MPK6 and TCMOp1 were down-regulated in root samples. The roots and leaves of the tiny millet OLM-203 genotype expressed 36 up-regulated and 21 down-regulated serine transcripts, respectively. Gene annotations for leaf samples were classified as having "molecular function" (46%), "cellular component" (19%), and "biological process" (35%), while root sample gene annotations were categorized as having "biological process" (573 contigs), "molecular function" (401 contigs), and "cellular components" (166 contigs). Noteworthy, polyamines play a crucial role in drought stress tolerance in the genotype, and it was found that top ten DEGs encoding for polyamines were common in two tissues (leaf and root). Collectively, transcriptomics profiling (RNA-seq) unveiled transcriptional stability drought stress provide a new insight in underlying modus of operandi in little millet genotype "OLM-203/Tarini" in response to heat stress.
Collapse
Affiliation(s)
| | - R S Tomar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Padhiyar Sm
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Kheni Jasminkumar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Gulwe Ashish
- Department of Bioinformatics, Sub Campus Latur, Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Nitin Mahendra Chauhan
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia
| | | | - Vijay Upadhye
- Research and Development Cell (RDC), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Kingdom of Saudi Arabia
| | - Laxmikant Kamble
- Deputy Director and Associate Professor (CD4D), Parul University, Vadodara, Gujarat, India
- Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Sunil Tulshiram Hajare
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia.
| |
Collapse
|
3
|
Daly P, Zhou D, Shen D, Chen Y, Xue T, Chen S, Zhang Q, Zhang J, McGowan J, Cai F, Pang G, Wang N, Sheikh TMM, Deng S, Li J, Soykam HO, Kara I, Fitzpatrick DA, Druzhinina IS, Bayram Akcapinar G, Wei L. Genome of Pythium myriotylum Uncovers an Extensive Arsenal of Virulence-Related Genes among the Broad-Host-Range Necrotrophic Pythium Plant Pathogens. Microbiol Spectr 2022; 10:e0226821. [PMID: 35946960 PMCID: PMC9430622 DOI: 10.1128/spectrum.02268-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
The Pythium (Peronosporales, Oomycota) genus includes devastating plant pathogens that cause widespread diseases and severe crop losses. Here, we have uncovered a far greater arsenal of virulence factor-related genes in the necrotrophic Pythium myriotylum than in other Pythium plant pathogens. The genome of a plant-virulent P. myriotylum strain (~70 Mb and 19,878 genes) isolated from a diseased rhizome of ginger (Zingiber officinale) encodes the largest repertoire of putative effectors, proteases, and plant cell wall-degrading enzymes (PCWDEs) among the studied species. P. myriotylum has twice as many predicted secreted proteins than any other Pythium plant pathogen. Arrays of tandem duplications appear to be a key factor of the enrichment of the virulence factor-related genes in P. myriotylum. The transcriptomic analysis performed on two P. myriotylum isolates infecting ginger leaves showed that proteases were a major part of the upregulated genes along with PCWDEs, Nep1-like proteins (NLPs), and elicitin-like proteins. A subset of P. myriotylum NLPs were analyzed and found to have necrosis-inducing ability from agroinfiltration of tobacco (Nicotiana benthamiana) leaves. One of the heterologously produced infection-upregulated putative cutinases found in a tandem array showed esterase activity with preferences for longer-chain-length substrates and neutral to alkaline pH levels. Our results allow the development of science-based targets for the management of P. myriotylum-caused disease, as insights from the genome and transcriptome show that gene expansion of virulence factor-related genes play a bigger role in the plant parasitism of Pythium spp. than previously thought. IMPORTANCE Pythium species are oomycetes, an evolutionarily distinct group of filamentous fungus-like stramenopiles. The Pythium genus includes several pathogens of important crop species, e.g., the spice ginger. Analysis of our genome from the plant pathogen Pythium myriotylum uncovered a far larger arsenal of virulence factor-related genes than found in other Pythium plant pathogens, and these genes contribute to the infection of the plant host. The increase in the number of virulence factor-related genes appears to have occurred through the mechanism of tandem gene duplication events. Genes from particular virulence factor-related categories that were increased in number and switched on during infection of ginger leaves had their activities tested. These genes have toxic activities toward plant cells or activities to hydrolyze polymeric components of the plant. The research suggests targets to better manage diseases caused by P. myriotylum and prompts renewed attention to the genomics of Pythium plant pathogens.
Collapse
Affiliation(s)
- Paul Daly
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Dongmei Zhou
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yifan Chen
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Taiqiang Xue
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Siqiao Chen
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Qimeng Zhang
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinfeng Zhang
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jamie McGowan
- Genome Evolution Laboratory, Maynooth University, Maynooth, Ireland
| | - Feng Cai
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Guan Pang
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
| | - Nan Wang
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Taha Majid Mahmood Sheikh
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Sheng Deng
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jingjing Li
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hüseyin Okan Soykam
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irem Kara
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | | | - Irina S. Druzhinina
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China
- Department of Accelerated Taxonomy, The Royal Botanic Gardens Kew, London, United Kingdom
| | - Günseli Bayram Akcapinar
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Lihui Wei
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| |
Collapse
|
4
|
Satheesh GR, Koyyappurath S, Varghese L, Thomas G. Genome and Transcriptome Sequence Resources and Effector Repertoire of Pythium myriotylum Drechsler. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:715-718. [PMID: 35834413 DOI: 10.1094/mpmi-07-21-0165-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Gayathri R Satheesh
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India
| | - Sayuj Koyyappurath
- Department of Biotechnology, Cochin University of Science and Technology, Cochin, 682022, Kerala, India
| | - Lini Varghese
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India
| | - George Thomas
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India
| |
Collapse
|
5
|
Abstract
Root rot diseases remain a major global threat to the productivity of agricultural crops. They are usually caused by more than one type of pathogen and are thus often referred to as a root rot complex. Fungal and oomycete species are the predominant participants in the complex, while bacteria and viruses are also known to cause root rot. Incorporating genetic resistance in cultivated crops is considered the most efficient and sustainable solution to counter root rot, however, resistance is often quantitative in nature. Several genetics studies in various crops have identified the quantitative trait loci associated with resistance. With access to whole genome sequences, the identity of the genes within the reported loci is becoming available. Several of the identified genes have been implicated in pathogen responses. However, it is becoming apparent that at the molecular level, each pathogen engages a unique set of proteins to either infest the host successfully or be defeated or contained in attempting so. In this review, a comprehensive summary of the genes and the potential mechanisms underlying resistance or susceptibility against the most investigated root rots of important agricultural crops is presented.
Collapse
|
6
|
Sukumari Nath V, Kumar Mishra A, Kumar A, Matoušek J, Jakše J. Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop ( Humulus Lupulus L.). Viruses 2019; 11:v11050419. [PMID: 31060295 PMCID: PMC6563305 DOI: 10.3390/v11050419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
Transcription factors (TFs) play a major role in controlling gene expression by intricately regulating diverse biological processes such as growth and development, the response to external stimuli and the activation of defense responses. The systematic identification and classification of TF genes are essential to gain insight into their evolutionary history, biological roles, and regulatory networks. In this study, we performed a global mining and characterization of hop TFs and their involvement in Citrus bark cracking viroid CBCVd infection by employing a digital gene expression analysis. Our systematic analysis resulted in the identification of a total of 3,818 putative hop TFs that were classified into 99 families based on their conserved domains. A phylogenetic analysis classified the hop TFs into several subgroups based on a phylogenetic comparison with reference TF proteins from Arabidopsis thaliana providing glimpses of their evolutionary history. Members of the same subfamily and subgroup shared conserved motif compositions. The putative functions of the CBCVd-responsive hop TFs were predicted using their orthologous counterparts in A. thaliana. The analysis of the expression profiling of the CBCVd-responsive hop TFs revealed a massive differential modulation, and the expression of the selected TFs was validated using qRT-PCR. Together, the comprehensive integrated analysis in this study provides better insights into the TF regulatory networks associated with CBCVd infections in the hop, and also offers candidate TF genes for improving the resistance in hop against viroids.
Collapse
Affiliation(s)
- Vishnu Sukumari Nath
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Ajay Kumar Mishra
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Atul Kumar
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Jaroslav Matoušek
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|