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Quesada-Ocampo LM, Parada-Rojas CH, Hansen Z, Vogel G, Smart C, Hausbeck MK, Carmo RM, Huitema E, Naegele RP, Kousik CS, Tandy P, Lamour K. Phytophthora capsici: Recent Progress on Fundamental Biology and Disease Management 100 Years After Its Description. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:185-208. [PMID: 37257056 DOI: 10.1146/annurev-phyto-021622-103801] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Phytophthora capsici is a destructive oomycete pathogen of vegetable, ornamental, and tropical crops. First described by L.H. Leonian in 1922 as a pathogen of pepper in New Mexico, USA, P. capsici is now widespread in temperate and tropical countries alike. Phytophthora capsici is notorious for its capability to evade disease management strategies. High genetic diversity allows P. capsici populations to overcome fungicides and host resistance, the formation of oospores results in long-term persistence in soils, zoospore differentiation in the presence of water increases epidemic potential, and a broad host range maximizes economic losses and limits the effectiveness of crop rotation. The severity of disease caused by P. capsici and management challenges have led to numerous research efforts in the past 100 years. Here, we discuss recent findings regarding the biology, genetic diversity, disease management, fungicide resistance, host resistance, genomics, and effector biology of P. capsici.
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Affiliation(s)
- L M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - C H Parada-Rojas
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - Z Hansen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - G Vogel
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - C Smart
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - M K Hausbeck
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - R M Carmo
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
| | - E Huitema
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - R P Naegele
- Sugarbeet and Bean Research Unit, USDA, ARS, East Lansing, Michigan, USA
| | - C S Kousik
- US Vegetable Laboratory, USDA, ARS, Charleston, South Carolina, USA
| | - P Tandy
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - K Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
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Sapkota S, Burlakoti RR, Lubberts M, Lamour K. Genome resources and whole genome resequencing of Phytophthora rubi isolates from red raspberry. FRONTIERS IN PLANT SCIENCE 2023; 14:1161864. [PMID: 37457337 PMCID: PMC10339809 DOI: 10.3389/fpls.2023.1161864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/15/2023] [Indexed: 07/18/2023]
Abstract
Phytophthora rubi is a primary causal agent of Phytophthora root rot and wilting of raspberry (Rubus idaeus L.) worldwide. The disease is a major concern for raspberry growers in Canada and USA. To date, no information is available on genomic diversity of P. rubi population from raspberry in Canada. Using a PCR-free library prep with dual-indexing for an Illumina HiSEQX running a 2x150 bp configuration, we generated whole genome sequence data of P. rubi isolates (n = 25) recovered during 2018 to 2020 from nine fields, four locations and four cultivars of raspberry growing areas of British Columbia, Canada. The assembled genome of 24 isolates of P. rubi averaged 8,541 scaffolds, 309× coverage, and 65,960,000 bp. We exploited single nucleotide polymorphisms (SNPs) obtained from whole genome sequence data to analyze the genome structure and genetic diversity of the P. rubi isolates. Low heterozygosity among the 72% of pathogen isolates and standardized index of association revealed that those isolates were clonal. Principal component analysis, discriminant analysis of principal component, and phylogenetic tree revealed that P. rubi isolates clustered with the raspberry specific cultivars. This study provides novel resources and insight into genome structure, genetic diversity, and reproductive biology of P rubi isolated from red raspberry. The availability of the P. rubi genomes also provides valuable resources for future comparative genomic and evolutionary studies for oomycetes pathogens.
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Affiliation(s)
- Sanjib Sapkota
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC, Canada
| | - Rishi R. Burlakoti
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, BC, Canada
| | - Mark Lubberts
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
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Maillot G, Szadkowski E, Massire A, Brunaud V, Rigaill G, Caromel B, Chadœuf J, Bachellez A, Touhami N, Hein I, Lamour K, Balzergue S, Lefebvre V. Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper. FRONTIERS IN PLANT SCIENCE 2022; 13:980587. [PMID: 36479518 PMCID: PMC9721114 DOI: 10.3389/fpls.2022.980587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper (Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici.
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Affiliation(s)
| | | | | | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- LaMME, Université d'Evry Val d'Essonne, INRAE, Evry, France
| | | | | | | | | | - Ingo Hein
- Division Plant Sciences at the JHI, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute (JHI), Dundee, United Kingdom
| | - Kurt Lamour
- INRAE, GAFL, Montfavet, France
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
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Siegenthaler TB, Lamour K, Hansen ZR. Population structure of Phytophthora capsici in the state of Tennessee. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01769-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractThe plant pathogen Phytophthora capsici can be found all throughout the USA, and the population genetics of this organism have been studied within many of these states. Until now, no work has been done in the state of Tennessee to investigate the population structure and genetics of P. capsici found there. The population structure of P. capsici was explored using 296 isolates collected from five counties in Tennessee in 2004, 2007, 2018, and 2019. Samples were genotyped using 39 single nucleotide polymorphism (SNP) genetic markers. Multiple analyses indicate that the population structure of P. capsici in Tennessee exists in isolated clusters structured by geography. Geographically separate populations were genetically distinct, suggesting there is limited or no outcrossing among populations, but there is significant sexual reproduction occurring within populations. These findings corroborate previous studies of P. capsici throughout the midwestern and northeastern USA, where populations are generally sexually reproducing and structured by geography. This study provides the first characterization of P. capsici population structure in Tennessee.
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Bhai RS, Jeevalatha A, Biju CN, Vinitha KB, Cissin J, Rosana OB, Fayad A, Praveena R, Anandaraj M, Eapen SJ. Sympatric occurrence of sibling Phytophthora species associated with foot rot disease of black pepper in India. Braz J Microbiol 2022; 53:801-818. [PMID: 35199325 PMCID: PMC9151956 DOI: 10.1007/s42770-022-00716-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Foot rot disease caused by Phytophthora capsici is a serious threat to black pepper cultivation in India and globally. High diversity exists among the Phytophthora isolates of black pepper and hence detailed investigations of their morphology and phylogenetic taxonomy were carried out in the present study. In order to resolve the diversity, 182 isolates of Phytophthora, collected from different black pepper-growing tracts of South India during 1998-2013 and maintained in the National Repository of Phytophthora at ICAR-Indian Institute of Spices Research, Kozhikode, were subjected to morphological, molecular and phylogenetic characterization. Morphologically all the isolates were long pedicellate with umbellate/simple sympodial sporangiophores and papillate sporangia with l/b ranging from 1.63 to 2.55 µm. Maximum temperature for the growth was ~ 34 °C. Chlamydospores were observed in "tropicalis" group, whereas they were absent in "capsici" group. Initial molecular studies using internal transcribed spacer (ITS) marker gene showed two clear cut lineages-"capsici-like" and "tropicalis-like" groups among them. Representative isolates from each group were subjected to host differential test, multilocus sequence typing (MLST) and phylogeny studies. MLST analysis of seven nuclear genes (60S ribosomal protein L10, beta-tubulin, elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA and TigA gene fusion protein) clearly delineated black pepper Phytophthora isolates into two distinct species-P. capsici and P. tropicalis. On comparing with type strains from ATCC, it was found that the type strains of P. capsici and P. tropicalis differed from black pepper isolates in their infectivity on black pepper. The high degree of genetic polymorphism observed in black pepper Phytophthora isolates is an indication of the selection pressure they are subjected to in the complex habitat which ultimately may lead to speciation. So based on the extensive analysis, it is unambiguously proved that the foot rot disease of black pepper in India is predominantly caused by two species of Phytophthora, viz. P. capsici and P. tropicalis. Presence of multiple species of Phytophthora in the black pepper agro-ecosystem warrants a revisit to the control strategy being adopted for managing this serious disease. The silent molecular evolution taking place in such an ecological niche needs to be critically studied for the sustainable management of foot rot disease.
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Affiliation(s)
- R. Suseela Bhai
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - A. Jeevalatha
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - C. N. Biju
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - K. B. Vinitha
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - Jose Cissin
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - O. B. Rosana
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - A. Fayad
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - R. Praveena
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - M. Anandaraj
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
| | - Santhosh J. Eapen
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala 673012 India
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Hu J, Shrestha S, Zhou Y, Mudge J, Liu X, Lamour K. Dynamic Extreme Aneuploidy (DEA) in the vegetable pathogen Phytophthora capsici and the potential for rapid asexual evolution. PLoS One 2020; 15:e0227250. [PMID: 31910244 PMCID: PMC6946123 DOI: 10.1371/journal.pone.0227250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/16/2019] [Indexed: 11/27/2022] Open
Abstract
Oomycete plant pathogens are difficult to control and routine genetic research is challenging. A major problem is instability of isolates. Here we characterize >600 field and single zoospore isolates of Phytophthora capsici for inheritance of mating type, sensitivity to mefenoxam, chromosome copy number and heterozygous allele frequencies. The A2 mating type was highly unstable with 26% of 241 A2 isolates remaining A2. The A1 mating type was stable. Isolates intermediately resistant to mefenoxam produced fully resistant single-spore progeny. Sensitive isolates remained fully sensitive. Genome re-sequencing of single zoospore isolates revealed extreme aneuploidy; a phenomenon dubbed Dynamic Extreme Aneuploidy (DEA). DEA is characterized by the asexual inheritance of diverse intra-genomic combinations of chromosomal ploidy ranging from 2N to 3N and heterozygous allele frequencies that do not strictly correspond to ploidy. Isolates sectoring on agar media showed dramatically altered heterozygous allele frequencies. DEA can explain the rapid increase of advantageous alleles (e.g. drug resistance), mating type switches and copy neutral loss of heterozygosity (LOH). Although the mechanisms driving DEA are unknown, it can play an important role in adaptation and evolution and seriously hinders all aspects of P. capsici research.
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Affiliation(s)
- Jian Hu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Yuxin Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Xili Liu
- College of Plant Pathology, China Agricultural University, Beijing, China
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Barchenger DW, Sheu ZM, Kumar S, Lin SW, Burlakoti RR, Bosland PW. Race Characterization of Phytophthora Root Rot on Capsicum in Taiwan as a Basis for Anticipatory Resistance Breeding. PHYTOPATHOLOGY 2018; 108:964-971. [PMID: 29484915 DOI: 10.1094/phyto-08-17-0289-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peppers (Capsicum sp.) are an increasingly important crop because of their use as a vegetable, spice, and food colorant. The oomycete Phytophthora capsici is one of the most devastating pathogens to pepper production worldwide, causing more than $100 million in losses annually. Developing cultivars resistant to P. capsici is challenging because of the many physiological races that exist and new races that are continuously evolving. This problem is confounded by the lack of a universal system of race characterization. As a basis to develop a global anticipatory breeding program, New Mexico recombinant inbred lines (NMRILs) functioned as a host differential for Phytophthora root rot to characterize the race structure of P. capsici populations in Taiwan. Using the NMRILs, 24 new races were identified, illustrating the utility and usefulness of the NMRILs for anticipatory breeding. Virulence of P. capsici was observed to be geographically specific and in two virulence clusters. Interestingly, all but two isolates collected in 2016 were the A2 mating type, which is a shift from the predominantly A1 mating type isolates collected prior to 2008. The NMRILs host differential provides an approach for scientists to work together on a global scale when breeding for resistance as well as on a local level for regional gene deployment. Additionally, we propose that the current race numbering system, which has no biological meaning, be supplemented with the virulence phenotype, based on the susceptible NMRILs to a given isolate. This work provides insights into the population dynamics of P. capsici and interactions within the highly complex Capsicum-Phytophthora pathosystem, and offers a basis for similar research in other crops.
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Affiliation(s)
- Derek W Barchenger
- First and sixth authors: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces; and first, second, third, fourth, and fifth: World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Zong-Ming Sheu
- First and sixth authors: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces; and first, second, third, fourth, and fifth: World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Sanjeet Kumar
- First and sixth authors: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces; and first, second, third, fourth, and fifth: World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Shih-Wen Lin
- First and sixth authors: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces; and first, second, third, fourth, and fifth: World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Rishi R Burlakoti
- First and sixth authors: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces; and first, second, third, fourth, and fifth: World Vegetable Center, Shanhua, Tainan, Taiwan
| | - Paul W Bosland
- First and sixth authors: Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces; and first, second, third, fourth, and fifth: World Vegetable Center, Shanhua, Tainan, Taiwan
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Barchenger DW, Lamour KH, Bosland PW. Challenges and Strategies for Breeding Resistance in Capsicum annuum to the Multifarious Pathogen, Phytophthora capsici. FRONTIERS IN PLANT SCIENCE 2018; 9:628. [PMID: 29868083 PMCID: PMC5962783 DOI: 10.3389/fpls.2018.00628] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Phytophthora capsici is the most devastating pathogen for chile pepper production worldwide and current management strategies are not effective. The population structure of the pathogen is highly variable and few sources of widely applicable host resistance have been identified. Recent genomic advancements in the host and the pathogen provide important insights into the difficulties reported by epidemiological and physiological studies published over the past century. This review highlights important challenges unique to this complex pathosystem and suggests strategies for resistance breeding to help limit losses associated with P. capsici.
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Affiliation(s)
- Derek W. Barchenger
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Kurt H. Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
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Genetic diversity of Phytophthora capsici recovered from Massachusetts between 1997 and 2014. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1334-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Barchenger DW, Lamour KH, Sheu ZM, Shrestha S, Kumar S, Lin SW, Burlakoti R, Bosland PW. Intra- and Intergenomic variation of Ploidy and Clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1330-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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