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Pérez-Hedo M, Gallego-Giraldo C, Forner-Giner MÁ, Ortells-Fabra R, Urbaneja A. Plant volatile-triggered defense in citrus against biotic stressors. FRONTIERS IN PLANT SCIENCE 2024; 15:1425364. [PMID: 39049855 PMCID: PMC11266131 DOI: 10.3389/fpls.2024.1425364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Plants employ sophisticated defense mechanisms, including releasing volatile organic compounds, to defend against biotic and abiotic stresses. These compounds play a crucial role in plant defense by attracting natural enemies and facilitating communication between plants to activate defense mechanisms. However, there has been no research on how exposure to these compounds activates defense mechanisms in citrus plants. To elucidate the underlying mechanisms governing citrus defensive activation, we conducted a molecular analysis of the rootstock Citrange carrizo [a hybrid of Citrus sinensis × Poncirus trifoliata] in response to defense activation by the volatile (Z)-3-hexenyl propanoate [(Z)-3-HP], utilizing a groundbreaking transcriptomic analysis involving the genomes of both parental species. Our results revealed significant gene expression changes, notably the overexpression of genes related to plant immunity, antioxidant activity, defense against herbivores, and tolerance to abiotic stress. Significantly, P. trifoliata contributed most notably to the hybrid's gene expression profile in response to (Z)-3-HP. Additionally, plants exposed to (Z)-3-HP repelled several citrus pests, attracted natural predators, and led to diminished performance of two key citrus pests. Our study emphasizes the complex molecular basis of volatile-triggered defenses in citrus and highlights the potential of plant volatiles in pest control strategies.
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Affiliation(s)
- Meritxell Pérez-Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Moncada, Valencia, Spain
| | - Carolina Gallego-Giraldo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Moncada, Valencia, Spain
| | - María Ángeles Forner-Giner
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Citricultura y Producción Vegetal, Moncada, Valencia, Spain
| | - Raúl Ortells-Fabra
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Moncada, Valencia, Spain
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Moncada, Valencia, Spain
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Singh K, Huff M, Liu J, Park JW, Rickman T, Keremane M, Krueger RR, Kunta M, Roose ML, Dardick C, Staton M, Ramadugu C. Chromosome-Scale, De Novo, Phased Genome Assemblies of Three Australian Limes: Citrus australasica, C. inodora, and C. glauca. PLANTS (BASEL, SWITZERLAND) 2024; 13:1460. [PMID: 38891269 PMCID: PMC11174732 DOI: 10.3390/plants13111460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
Huanglongbing (HLB) is a severe citrus disease worldwide. Wild Australian limes like Citrus australasica, C. inodora, and C. glauca possess beneficial HLB resistance traits. Individual trees of the three taxa were extensively used in a breeding program for over a decade to introgress resistance traits into commercial-quality citrus germplasm. We generated high-quality, phased, de novo genome assemblies of the three Australian limes using PacBio long-read sequencing. The genome assembly sizes of the primary and alternate haplotypes were determined for C. australasica (337 Mb/335 Mb), C. inodora (304 Mb/299 Mb), and C. glauca (376 Mb/379 Mb). The nine chromosome-scale scaffolds included 86-91% of the genome sequences generated. The integrity and completeness of the assembled genomes were estimated to be at 97.2-98.8%. Gene annotation studies identified 25,461 genes in C. australasica, 27,665 in C. inodora, and 30,067 in C. glauca. Genes belonging to 118 orthogroups were specific to Australian lime genomes compared to other citrus genomes analyzed. Significantly fewer canonical resistance (R) genes were found in C. inodora and C. glauca (319 and 449, respectively) compared to C. australasica (576), C. clementina (579), and C. sinensis (651). Similar patterns were observed for other gene families associated with potential HLB resistance, including Phloem protein 2 (PP2) and Callose synthase (CalS) genes predicted in the Australian lime genomes. The genomic information on Australian limes developed in the present study will help understand the genetic basis of HLB resistance.
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Affiliation(s)
- Khushwant Singh
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
| | - Matthew Huff
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Jianyang Liu
- Innovative Fruit Production, Improvement, and Protection, Appalachian Fruit Research Station, USDA-ARS, Kearneysville, WV 25430, USA; (J.L.); (C.D.)
| | - Jong-Won Park
- Citrus Center, Texas A&M University-Kingsville, Weslaco, TX 78599, USA; (J.-W.P.); (M.K.)
| | - Tara Rickman
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Manjunath Keremane
- National Clonal Germplasm Repository for Citrus and Dates, USDA-ARS, Riverside, CA 92507, USA; (M.K.); (R.R.K.)
| | - Robert R. Krueger
- National Clonal Germplasm Repository for Citrus and Dates, USDA-ARS, Riverside, CA 92507, USA; (M.K.); (R.R.K.)
| | - Madhurababu Kunta
- Citrus Center, Texas A&M University-Kingsville, Weslaco, TX 78599, USA; (J.-W.P.); (M.K.)
| | - Mikeal L. Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
| | - Chris Dardick
- Innovative Fruit Production, Improvement, and Protection, Appalachian Fruit Research Station, USDA-ARS, Kearneysville, WV 25430, USA; (J.L.); (C.D.)
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (M.H.); (T.R.); (M.S.)
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; (K.S.); (M.L.R.)
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Liu C, Chang X, Li F, Yan Y, Zuo X, Huang G, Li R. Transcriptome analysis of Citrus sinensis reveals potential responsive events triggered by Candidatus Liberibacter asiaticus. PROTOPLASMA 2024; 261:499-512. [PMID: 38092896 DOI: 10.1007/s00709-023-01911-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/01/2023] [Indexed: 04/18/2024]
Abstract
Citrus Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), is a devastating immune-mediated disorder that has a detrimental effect on the citrus industry, with the distinguishing feature being an eruption of reactive oxygen species (ROS). This study explored the alterations in antioxidant enzyme activity, transcriptome, and RNA editing events of organelles in C. sinensis during CLas infection. Results indicated that there were fluctuations in the performance of antioxidant enzymes, such as ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), peroxidase (POD), and superoxide dismutase (SOD), in plants affected by HLB. Transcriptome analysis revealed 3604 genes with altered expression patterns between CLas-infected and healthy samples, including those associated with photosynthesis, biotic interactions, and phytohormones. Samples infected with CLas showed a decrease in the expression of most genes associated with photosynthesis and gibberellin metabolism. It was discovered that RNA editing frequency and the expression level of various genes in the chloroplast and mitochondrion genomes were affected by CLas infection. Our findings provide insights into the inhibition of photosynthesis, gibberellin metabolism, and antioxidant enzymes during CLas infection in C. sinensis.
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Affiliation(s)
- Chang Liu
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Xiaopeng Chang
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Fuxuan Li
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yana Yan
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Xiru Zuo
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Guiyan Huang
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
| | - Ruimin Li
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
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Nakandala U, Furtado A, Masouleh AK, Smith MW, Williams DC, Henry RJ. The genome of Citrus australasica reveals disease resistance and other species specific genes. BMC PLANT BIOLOGY 2024; 24:260. [PMID: 38594608 PMCID: PMC11005238 DOI: 10.1186/s12870-024-04988-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The finger lime (Citrus australasica), one of six Australian endemic citrus species shows a high natural phenotypic diversity and novel characteristics. The wide variation and unique horticultural features have made this lime an attractive candidate for domestication. Currently no haplotype resolved genome is available for this species. Here we present a high quality, haplotype-resolved reference genome for this species using PacBio HiFi and Hi-C sequencing. RESULTS Hifiasm assembly and SALSA scaffolding resulted in a collapsed genome size of 344.2 Mb and 321.1 Mb and 323.2 Mb size for the two haplotypes. The nine pseudochromosomes of the collapsed genome had an N50 of 35.2 Mb, 99.1% genome assembly completeness and 98.9% gene annotation completeness (BUSCO). A total of 41,304 genes were predicted in the nuclear genome. Comparison with C. australis revealed that 13,661 genes in pseudochromosomes were unique in C. australasica. These were mainly involved in plant-pathogen interactions, stress response, cellular metabolic and developmental processes, and signal transduction. The two genomes showed a syntenic arrangement at the chromosome level with large structural rearrangements in some chromosomes. Genetic variation among five C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identified in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome. CONCLUSIONS The genome of C. australasica present in this study is of high quality and contiguity. This genome helps deepen our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.
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Affiliation(s)
- Upuli Nakandala
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia
| | - Ardashir Kharabian Masouleh
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia
| | - Malcolm W Smith
- Department of Agriculture and Fisheries, Bundaberg Research Station, Bundaberg, QLD, 4670, Australia
| | | | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia.
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Gao C, Li C, Li Z, Liu Y, Li J, Guo J, Mao J, Fang F, Wang C, Deng X, Zheng Z. Comparative transcriptome profiling of susceptible and tolerant citrus species at early and late stage of infection by " Candidatus Liberibacter asiaticus". FRONTIERS IN PLANT SCIENCE 2023; 14:1191029. [PMID: 37389294 PMCID: PMC10301834 DOI: 10.3389/fpls.2023.1191029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/29/2023] [Indexed: 07/01/2023]
Abstract
Citrus Huanglongbing (HLB), caused by "Candidatus Liberibacter asiaticus" (CLas), is the most destructive disease threatening global citrus industry. Most commercial cultivars were susceptible to HLB, although some showed tolerant to HLB phenotypically. Identifying tolerant citrus genotypes and understanding the mechanism correlated with tolerance to HLB is essential for breeding citrus variety tolerance/resistance to HLB. In this study, the graft assay with CLas-infected bud were performed in four citrus genotypes, including Citrus reticulata Blanco, C. sinensis, C. limon, and C. maxima. HLB tolerance was observed in C. limon and C. maxima, while C. Blanco and C. sinensis were susceptible to HLB. The time-course transcriptomic analysis revealed a significant variation in differentially expressed genes (DEGs) related to HLB between susceptible and tolerant cultivar group at early and late infection stage. Functional analysis of DEGs indicated that the activation of genes involved in SA-mediated defense response, PTI, cell wall associated immunity, endochitinase, phenylpropanoid and alpha-linolenic/linoleic lipid metabolism played an important in the tolerance of C. limon and C. maxima to HLB at early infection stage. In addition, the overactive plant defense combined with the stronger antibacterial activity (antibacterial secondary and lipid metabolism) and the suppression of pectinesterase were contributed to the long-term tolerance to HLB in C. limon and C. maxima at late infection stage. Particularly, the activation of ROS scavenging genes (catalases and ascorbate peroxidases) could help to reduce HLB symptoms in tolerant cultivars. In contrast, the overexpression of genes involved in oxidative burst and ethylene metabolism, as well as the late inducing of defense related genes could lead to the early HLB symptom development in susceptible cultivars at early infection stage. The weak defense response and antibacterial secondary metabolism, and the induce of pectinesterase were responsible for sensitivity to HLB in C. reticulata Blanco and C. sinensis at late infection stage. This study provided new insights into the tolerance/sensitivity mechanism against HLB and valuable guidance for breeding of HLB-tolerant/resistant cultivars.
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Affiliation(s)
- Chenying Gao
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Cuixiao Li
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Ziyi Li
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Yaoxin Liu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
| | - Jiaming Li
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Jun Guo
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Jiana Mao
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Fang Fang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Cheng Wang
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Xiaoling Deng
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Zheng Zheng
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
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Estrella-Maldonado H, González-Cruz C, Matilde-Hernández C, Adame-García J, Santamaría JM, Santillán-Mendoza R, Flores-de la Rosa FR. Insights into the Molecular Basis of Huanglongbing Tolerance in Persian Lime ( Citrus latifolia Tan.) through a Transcriptomic Approach. Int J Mol Sci 2023; 24:ijms24087497. [PMID: 37108662 PMCID: PMC10144405 DOI: 10.3390/ijms24087497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Huanglongbing (HLB) is a vascular disease of Citrus caused by three species of the α-proteobacteria "Candidatus Liberibacter", with "Candidatus Liberibacter asiaticus" (CLas) being the most widespread and the one causing significant economic losses in citrus-producing regions worldwide. However, Persian lime (Citrus latifolia Tanaka) has shown tolerance to the disease. To understand the molecular mechanisms of this tolerance, transcriptomic analysis of HLB was performed using asymptomatic and symptomatic leaves. RNA-Seq analysis revealed 652 differentially expressed genes (DEGs) in response to CLas infection, of which 457 were upregulated and 195 were downregulated. KEGG analysis revealed that after CLas infection, some DEGs were present in the plant-pathogen interaction and in the starch and sucrose metabolism pathways. DEGs present in the plant-pathogen interaction pathway suggests that tolerance against HLB in Persian lime could be mediated, at least partly, by the ClRSP2 and ClHSP90 genes. Previous reports documented that RSP2 and HSP90 showed low expression in susceptible citrus genotypes. Regarding the starch and sucrose metabolism pathways, some genes were identified as being related to the imbalance of starch accumulation. On the other hand, eight biotic stress-related genes were selected for further RT-qPCR analysis to validate our results. RT-qPCR results confirmed that symptomatic HLB leaves had high relative expression levels of the ClPR1, ClNFP, ClDR27, and ClSRK genes, whereas the ClHSL1, ClRPP13, ClPDR1, and ClNAC genes were expressed at lower levels than those from HLB asymptomatic leaves. Taken together, the present transcriptomic analysis contributes to the understanding of the CLas-Persian lime interaction in its natural environment and may set the basis for developing strategies for the integrated management of this important Citrus disease through the identification of blanks for genetic improvement.
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Affiliation(s)
- Humberto Estrella-Maldonado
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Cong. Javier Rojo Gómez, Tlapacoyan C.P. 93600, Veracruz, Mexico
| | - Carlos González-Cruz
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Cong. Javier Rojo Gómez, Tlapacoyan C.P. 93600, Veracruz, Mexico
| | - Cristian Matilde-Hernández
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Cong. Javier Rojo Gómez, Tlapacoyan C.P. 93600, Veracruz, Mexico
| | - Jacel Adame-García
- Tecnológico Nacional de México, Campus Úrsulo Galván, Km 4.5 Carretera Cd. Cardel-Chachalacas, Úrsulo Galván C.P. 91667, Veracruz, Mexico
| | - Jorge M Santamaría
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ricardo Santillán-Mendoza
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Cong. Javier Rojo Gómez, Tlapacoyan C.P. 93600, Veracruz, Mexico
| | - Felipe Roberto Flores-de la Rosa
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Cong. Javier Rojo Gómez, Tlapacoyan C.P. 93600, Veracruz, Mexico
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