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Awan UA, Meng L, Xia S, Raza MF, Zhang Z, Zhang H. Isolation, fermentation, and formulation of entomopathogenic fungi virulent against adults of Diaphorina citri. PEST MANAGEMENT SCIENCE 2021; 77:4040-4053. [PMID: 33896118 DOI: 10.1002/ps.6429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/13/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Mycopesticides are important for integrated management of the Asian citrus psyllid, Diaphorina citri. However, there are few reports on the fermentation and formulation for mycopesticides with high virulence against D. citri. RESULTS From four different locations in South China, 12 fungal strains were isolated and classified into Beauveria bassiana (two isolates), Fusarium fujikuroi (five isolates), and Cordyceps javanica (five isolates) based on the phylogenetic analysis of ITS1-5.8S rDNA-ITS4 and morphology of colonies and conidia. Based on the highest initial virulence (86.52 ± 2.35%) and best growth characteristics, F-HY002-ACPHali was further optimized for biphasic fermentation (7.85 ± 2.62 × 109 g-1 dry substrate) with soybean meal + cottonseed flour (1:1) as the solid substrate and full light as the light/dark cycle. Furthermore, the oil-based conidial formulation was optimized with sesame oil as an effective carrier, which significantly enhanced conidial shelf life up to 16 weeks at 26 °C and 4 °C, thermo-stress (50 °C) and UV-B stress resistance, and virulence against adults of D. citri with increased mortalities and decreased LT50 in comparison to that of unformulated conidia. CONCLUSION Our results not only provide a valuable native strain with high virulence against adults of D. citri, but also imply the soybean meal + cottonseed flour as valuable solid substrate, full-light exposure as environmental stimuli for solid-state fermentation, and the sesame oil as an effective carrier for the formulation of the C. javanica. These findings will facilitate the development of a potential mycopesticide for the biological control of Asian citrus psyllid.
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Affiliation(s)
- Umar Anwar Awan
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology (MOE), College of Plant Science and Technology, Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, China
| | - Lixue Meng
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Shuang Xia
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology (MOE), College of Plant Science and Technology, Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Fahim Raza
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology (MOE), College of Plant Science and Technology, Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, China
| | - Zhenyu Zhang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology (MOE), College of Plant Science and Technology, Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Zhang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology (MOE), College of Plant Science and Technology, Institute of Urban and Horticultural Entomology, Huazhong Agricultural University, Wuhan, China
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Das AK, Chichghare SA, Sharma SK, Kumar JPT, Singh S, Baranwal VK, Kumar A, Nerkar S. Genetic diversity and population structure of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing in India based on the prophage types. World J Microbiol Biotechnol 2021; 37:95. [PMID: 33963452 DOI: 10.1007/s11274-021-03057-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022]
Abstract
Huanglongbing (HLB), also known as 'citrus greening', is an extremely destructive disease of citrus worldwide. HLB is associated with three species of the fastidious proteobacterium, Candidatus Liberibacter asiaticus (CaLas), Ca. L. africanus and Ca. L. americanus with CaLas being the most widely distributed around the world and the only species detected and described so far in India, one of the major global citrus fruit producers. Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. Three types of prophages, Type 1, Type 2 and Type 3 have been identified and described in CaLas so far. In the present study, 441 CaLas isolates sampled across 18 Indian states were used for prophage typing. Based on detection of three prophage types by PCR, all the eight probable combinations of CaLas prophages were identified, including single Type 1 (26.5%), single Type 2 (18.8%), single Type 3 (1.4%), Type 1 + Type 2 (20.4%), Type 1 + Type 3 (12.5%), Type 2 + Type 3 (4.8%), Type 1 + Type 2 + Type 3 (11.3%) and None type (4.3%). Prophage types were confirmed by PCR amplicon sequencing and subsequent phylogenetic analysis. By discovery of all 3 prophages and based on genetic identity and genetic distance, CaLas populations from eighteen citrus growing states were separated into two major Prophage Typing Groups (PTGs): PTG1 and PTG2. The PTG1 comprised of CaLas from North-West India and PTG2 from rest of the country (North-East, Central and South India), and both major groups were further divided into two (PTG1-A, PTG1-B) and three (PTG2-A, PTG2-B and PTG2-C) subgroups respectively. The findings of CaLas population patterns provide evidence for independent origins of HLB-associated CaLas. CRISPR (clustered regularly interspaced short palindromic repeats) array was also detected in CaLas isolates. This is the first report evaluating the genetic variation of a large population of CaLas bacterium in India using the PCR markers from the prophage regions which would certainly assist the ongoing HLB management efforts in India.
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Affiliation(s)
- Ashis K Das
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India.
| | - Subham A Chichghare
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Susheel K Sharma
- ICAR Research Complex for NEH Region, Manipur Centre, Imphal, 795004, India
| | - J Prasanth Tej Kumar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, India
| | - Virendra K Baranwal
- Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ashok Kumar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
| | - Sagar Nerkar
- Plant Pathology Lab, ICAR-Central Citrus Research Institute, Amravati Road, Nagpur, 440033, India
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Predictions of potential geographical distribution of Diaphorina citri (Kuwayama) in China under climate change scenarios. Sci Rep 2020; 10:9202. [PMID: 32513980 PMCID: PMC7280263 DOI: 10.1038/s41598-020-66274-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/11/2020] [Indexed: 11/09/2022] Open
Abstract
Climate change significantly affects geographic distribution of plants pests and diseases worldwide. Understanding the influence of future climate change on the suitable areas of Diaphorina citri (Kuwayama) in our country and taking timely countermeasures are crucial for improving the effectiveness of control of pest. Based on the occurrence points of D. citri and the selected environmental variables, the potential suitable areas of this pest under climate change scenarios in China were predicted by using MaxEnt and GIS tools. Our results showed that the higly suitable area were mainly located in Guangxi, Guangdong, Fujian, Southern Zhejiang, Southern Jiangxi, Eastern Hunan, Southwestern Guizhou, and the area was 43.7 × 104 km2. Areas of moderate and low suitability were centered on areas of high suitability and radiate to the North successively, with an area of 59.28 × 104 km2 and 93.46 × 104 km2 respectively. From current to 2070 s, the areas of the highly suitable areas will increase, and the geometric center of the highly and total suitable areas will move to north under three climate change scenarios.
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da Silva PA, Fassini CG, Sampaio LS, Dequigiovanni G, Zucchi MI, Wulff NA. Genetic Diversity of ' Candidatus Liberibacter asiaticus' Revealed by Short Tandem Repeats and Prophage Typing Indicates Population Homogeneity in Brazil. PHYTOPATHOLOGY 2019; 109:960-971. [PMID: 30694114 DOI: 10.1094/phyto-08-18-0295-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
'Candidatus Liberibacter asiaticus' is the most common huanglongbing-associated bacteria, being present in Asia, South, Central, and North America. Genomic approaches enabled sequencing of 'Ca. L. asiaticus' genomes, allowing for a broader assessment of its genetic variability with the application of polymerase chain reaction (PCR)-based tools such as microsatellite or short tandem repeat (STR) analysis. Although these tools contributed to a detailed analysis of strains from Japan, China, and the United States, Brazilian strains were analyzed in either too few samples with several STRs or in several strains with only a single microsatellite and a single PCR marker. We used 573 'Ca. L. asiaticus' strains, mainly collected from São Paulo State (SPS), in our genetic analyses, employing three STRs and several prophage PCR markers. STR revealed a homogeneous population regardless of sampling year or geographic regions of SPS. Thirty-eight haplotypes were recognized with a predominance of VNTR_005 higher than 10 repeats, with VNTR_002 and VNTR_077 containing 11 and 8 repeats, respectively. This haplotype is indicated as class HE, which comprised 80.28% of strains. Classes HA and HB, predominant in Florida, were not found. A new genomic organization in the junction of prophages SC2 and SC1 is prevalent in Brazilian strains, indicating gene rearrangement and a widespread occurrence of a type 1 prophage as well as the presence of a type 2-like prophage. Our results indicate that 'Ca. L. asiaticus' populations are homogeneous and harbor a new genomic organization in prophages type 1 and 2.
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Affiliation(s)
| | - Camila Giacomo Fassini
- 1 Departamento de Pesquisa & Desenvolvimento-Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Laís Simões Sampaio
- 1 Departamento de Pesquisa & Desenvolvimento-Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Gabriel Dequigiovanni
- 2 Agência Paulista de Tecnologia dos Agronegócios, Polo Regional Centro-Sul, Rodovia SP 127, km 30, Piracicaba, SP, 13400-970 Brazil; and
| | - Maria Imaculada Zucchi
- 2 Agência Paulista de Tecnologia dos Agronegócios, Polo Regional Centro-Sul, Rodovia SP 127, km 30, Piracicaba, SP, 13400-970 Brazil; and
| | - Nelson Arno Wulff
- 1 Departamento de Pesquisa & Desenvolvimento-Fundecitrus, Araraquara, SP, 14807-040, Brazil
- 3 PPG Biotecnologia, IQ/UNESP Araraquara, SP, 14800-060, Brazil
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Chen Y, Li T, Zheng Z, Xu M, Deng X. Draft Whole-Genome Sequence of a " Candidatus Liberibacter asiaticus" Strain from Yunnan, China. Microbiol Resour Announc 2019; 8:e01413-18. [PMID: 30687827 PMCID: PMC6346159 DOI: 10.1128/mra.01413-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 11/22/2022] Open
Abstract
The draft genome sequence of "Candidatus Liberibacter asiaticus" strain YNJS7C, isolated from a navel orange tree in Yunnan Province, China, is presented here. The YNJS7C strain has a genome size of 1,258,986 bp, with a G+C content of 36.6%, 1,174 predicted open reading frames, and 53 RNA genes.
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Affiliation(s)
- Yanling Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Tao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zheng Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Meirong Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xiaoling Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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Wu F, Jiang H, Beattie GAC, Holford P, Chen J, Wallis CM, Zheng Z, Deng X, Cen Y. Population diversity of Diaphorina citri (Hemiptera: Liviidae) in China based on whole mitochondrial genome sequences. PEST MANAGEMENT SCIENCE 2018; 74:2569-2577. [PMID: 29688605 DOI: 10.1002/ps.5044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Diaphorina citri (Asian citrus psyllid; ACP) transmits 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing (HLB). ACP has been reported in 11 provinces/regions in China, yet its population diversity remains unclear. In this study, we evaluated ACP population diversity in China using representative whole mitochondrial genome (mitogenome) sequences. Additional mitogenome sequences outside China were also acquired and evaluated. RESULTS The sizes of the 27 ACP mitogenome sequences ranged from 14 986 to 15 030 bp. Along with three previously published mitogenome sequences, the 30 sequences formed three major mitochondrial groups (MGs): MG1, present in southwestern China and occurring at elevations above 1000 m; MG2, present in southeastern China and Southeast Asia (Cambodia, Indonesia, Malaysia, and Vietnam) and occurring at elevations below 180 m; and MG3, present in the USA and Pakistan. Single nucleotide polymorphisms in five genes (cox2, atp8, nad3, nad1 and rrnL) contributed mostly in the ACP diversity. Among these genes, rrnL had the most variation. CONCLUSION Mitogenome sequences analyses revealed two major phylogenetic groups of ACP present in China as well as a possible unique group present currently in Pakistan and the USA. The information could have significant implications for current ACP control and HLB management. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Fengnian Wu
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - Hongyan Jiang
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - G Andrew C Beattie
- School of Science and Health, Western Sydney University, Penrith, Australia
| | - Paul Holford
- School of Science and Health, Western Sydney University, Penrith, Australia
| | - Jianchi Chen
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Christopher M Wallis
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
| | - Zheng Zheng
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - Xiaoling Deng
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
| | - Yijing Cen
- Citrus Huanglongbing Research Laboratory/Laboratory of Insect Ecology, South China Agricultural University, Guangzhou, China
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Zheng Z, Chen J, Deng X. Historical Perspectives, Management, and Current Research of Citrus HLB in Guangdong Province of China, Where the Disease has been Endemic for Over a Hundred Years. PHYTOPATHOLOGY 2018; 108:1224-1236. [PMID: 30156499 DOI: 10.1094/phyto-07-18-0255-ia] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Citrus huanglongbing (HLB) is a highly destructive disease currently threatening citrus production worldwide. In China, the disease is exclusively associated with 'Candidatus Liberibacter asiaticus', a nonculturable proteobacterium. HLB was observed in Guangdong of China over a hundred years ago. Researchers and citrus growers have been battling with the disease through vigorous research and have exercised various control practices. Much of the early work was not well known outside China. This review is intended to fill in gaps of historical information by reviewing selected literature records. Along the way, the HLB system within southern China was evaluated. Emphases were on comparison of symptomatology, evolution of etiology, control practices, and impacts of using next-generation sequencing technology for 'Ca. L. asiaticus' research and detection.
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Affiliation(s)
- Zheng Zheng
- First and third authors: Laboratory of Citrus Huanglongbing Research, Department of Plant Pathology, South China Agricultural University, Guangzhou, China; and second author: San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA
| | - Jianchi Chen
- First and third authors: Laboratory of Citrus Huanglongbing Research, Department of Plant Pathology, South China Agricultural University, Guangzhou, China; and second author: San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA
| | - Xiaoling Deng
- First and third authors: Laboratory of Citrus Huanglongbing Research, Department of Plant Pathology, South China Agricultural University, Guangzhou, China; and second author: San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture-Agricultural Research Service, Parlier, CA
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Hu Y, Zhong X, Liu X, Lou B, Zhou C, Wang X. Comparative transcriptome analysis unveils the tolerance mechanisms of Citrus hystrix in response to 'Candidatus Liberibacter asiaticus' infection. PLoS One 2017; 12:e0189229. [PMID: 29232716 PMCID: PMC5726760 DOI: 10.1371/journal.pone.0189229] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 11/21/2017] [Indexed: 11/26/2022] Open
Abstract
Citrus Huanglongbing (HLB), a highly devastating citrus disease, is associated with 'Candidatus Liberibacter asiacitus' (CLas), a member of phloem-inhabiting α-proteobacteria. HLB can affect all cultivated citrus and no cure is currently available. Previous studies showed that Kaffir lime (Citrus hystrix), primarily grown in South Asia and Southeast Asia, was tolerant to HLB but the molecular mechanism remains unknown. In this study, gene expression profiling experiments were performed on HLB-tolerant C. hystrix and HLB-susceptible C. sinensis three months after inoculation with CLas using RNA-seq data. Differentially expressed genes (DEGs) in the two citrus cultivars were mainly involved in diverse cellular functions including carbohydrate metabolism, photosynthesis, cell wall metabolism, secondary metabolism, hormone metabolism and oxidation/reduction processes. Notably, starch synthesis and photosynthesis process were not disturbed in CLas-infected C. hystrix. Most of the DEGs involved in cell wall metabolism and secondary metabolism were up-regulated in C. hystrix. In addition, the activation of peroxidases, Cu/Zn-SOD and POD4, may also enhance the tolerance of C. hystrix to CLas. This study provides an insight into the host response of HLB-tolerant citrus cultivar to CLas. C. hystrix is potentially useful for HLB-tolerant/resistant citrus breeding in the future.
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Affiliation(s)
- Yan Hu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, P. R. China
- Ganzhou Bureau of Fruit Industry, Ganzhou, Jiangxi, P. R. China
| | - Xi Zhong
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, P. R. China
| | - Xuelu Liu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, P. R. China
| | - Binghai Lou
- Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi, P. R. China
| | - Changyong Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, P. R. China
| | - Xuefeng Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, P. R. China
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Zheng Z, Bao M, Wu F, Chen J, Deng X. Predominance of Single Prophage Carrying a CRISPR/cas System in "Candidatus Liberibacter asiaticus" Strains in Southern China. PLoS One 2016; 11:e0146422. [PMID: 26741827 PMCID: PMC4711790 DOI: 10.1371/journal.pone.0146422] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/16/2015] [Indexed: 11/22/2022] Open
Abstract
“Candidatus Liberibacter asiaticus” (CLas) is an uncultureable α-proteobacterium associated with citrus Huanglongbing (HLB, yellow shoot disease), a highly destructive disease affecting citrus production worldwide. HLB was observed in Guangdong Province of China over a hundred years ago and remains endemic there. Little is known about CLas biology due to its uncultureable nature. This study began with the genome sequence analysis of CLas Strain A4 from Guangdong in the prophage region. Within the two currently known prophage types, Type 1 (SC1-like) and Type 2 (SC2-like), A4 genome contained only a Type 2 prophage, CGdP2, namely. An analysis on CLas strains collected in Guangdong showed that Type 2 prophage dominated the bacterial population (82.6%, 71/86). An extended survey covering five provinces in southern China also revealed the predominance of single prophage (Type 1 or Type 2) in the CLas population (90.4%, 169/187). CLas strains with two and no prophage types accounted for 7.2% and 2.8%, respectively. In silico analyses on CGdP2 identified a CRISPR (clustered regularly interspaced short palindromic repeats)/cas (CRISPR-associated protein genes) system, consisting of four 22 bp repeats, three 23 bp spacers and 9 predicted cas. Similar CRISPR/cas systems were detected in all 10 published CLas prophages as well as 13 CLas field strains in southern China. Both Type 1 and Type 2 prophages shared almost identical sequences in spacer 1 and 3 but not spacer 2. Considering that the function of a CRISPR/cas system was to destroy invading DNA, it was hypothesized that a pre-established CLas prophage could use its CRISPR/cas system guided by spacer 1 and/or 3 to defeat the invasion of the other phage/prophage. This hypothesis explained the predominance of single prophage type in the CLas population in southern China. This is the first report of CRISPR/cas system in the “Ca. Liberibacter” genera.
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Affiliation(s)
- Zheng Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Peoples' Republic of China
- San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture–Agricultural Research Service, Parlier, California, United States of America
| | - Minli Bao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Peoples' Republic of China
| | - Fengnian Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Peoples' Republic of China
- San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture–Agricultural Research Service, Parlier, California, United States of America
| | - Jianchi Chen
- San Joaquin Valley Agricultural Sciences Center, United States Department of Agriculture–Agricultural Research Service, Parlier, California, United States of America
| | - Xiaoling Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Peoples' Republic of China
- * E-mail:
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Ghosh DK, Bhose S, Motghare M, Warghane A, Mukherjee K, Ghosh DK, Sharma AK, Ladaniya MS, Gowda S. Genetic Diversity of the Indian Populations of 'Candidatus Liberibacter asiaticus' Based on the Tandem Repeat Variability in a Genomic Locus. PHYTOPATHOLOGY 2015; 105:1043-1049. [PMID: 25760522 DOI: 10.1094/phyto-09-14-0253-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Citrus huanglongbing (HLB, citrus greening disease) is an extremely destructive disease affecting citrus and causes severe economic loss to the crop yield worldwide. The disease is caused by a phloem-limited, noncultured, gram-negative bacteria Candidatus Liberibacter spp., the widely present and most destructive species being 'Candidatus Liberibacter asiaticus'. Although the disease has been reported from almost all citrus growing regions of India, knowledge on the molecular variability of the pathogen 'Ca. L. asiaticus' populations from different geographical regions and cultivars is limited. In the present study, variability of the Indian 'Ca. L. asiaticus' based on the tandem repeats at the genomic locus CLIBASIA_01645 was characterized and categorized into four classes based on the tandem repeat number (TRN); Class I (TRN≤5), Class II (TRN>5≤10), Class III (TRN>10≤15), and Class IV (TRN>15). The study revealed that the Indian population of 'Ca. L. asiaticus' is more diverse than reported for Florida and Guangdong populations, which showed less diversity. While Florida and Guangdong populations were dominated by a TRN5 and TRN7 genotype, respectively, the Indian 'Ca. L. asiaticus' populations with TRN copy numbers 9, 10, 11, 12, and 13 were widely distributed throughout the country. Additionally, TRN2 and TRN17 genotypes were also observed among the Indian 'Ca. L. asiaticus' populations. The predominant 'Ca. L. asiaticus' genotypes from the northeastern region of India were TRN6 and TRN7 (53.12%) and surprisingly similar to neighboring South China populations. Preliminary results showed absence of preference of citrus cultivars to any specific 'Ca. L. asiaticus' genotype.
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Affiliation(s)
- Dilip Kumar Ghosh
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Sumit Bhose
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Manali Motghare
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Ashish Warghane
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Krishanu Mukherjee
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Dipak Kumar Ghosh
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Ashwani Kumar Sharma
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Milind Shivratan Ladaniya
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
| | - Siddarame Gowda
- First, second, third, fourth, and eighth authors: National Research Centre for Citrus, PB 464, P.O. Shankarnagar, Nagpur 440010, India; fifth author: The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine 32080; sixth author: Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, India; seventh author: Department of Biotechnology, Indian Institute of Technology, Roorkee 247 667, India; and ninth author: University of Florida, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred 33850
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Puttamuk T, Zhou L, Thaveechai N, Zhang S, Armstrong CM, Duan Y. Genetic diversity of Candidatus Liberibacter asiaticus based on two hypervariable effector genes in Thailand. PLoS One 2014; 9:e112968. [PMID: 25437428 PMCID: PMC4249863 DOI: 10.1371/journal.pone.0112968] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/16/2014] [Indexed: 01/22/2023] Open
Abstract
Huanglongbing (HLB), also known as citrus greening, is one of the most destructive diseases of citrus worldwide. HLB is associated with three species of 'Candidatus Liberibacter' with 'Ca. L. asiaticus' (Las) being the most widely distributed around the world, and the only species detected in Thailand. To understand the genetic diversity of Las bacteria in Thailand, we evaluated two closely-related effector genes, lasAI and lasAII, found within the Las prophages from 239 infected citrus and 55 infected psyllid samples collected from different provinces in Thailand. The results indicated that most of the Las-infected samples collected from Thailand contained at least one prophage sequence with 48.29% containing prophage 1 (FP1), 63.26% containing prophage 2 (FP2), and 19.38% containing both prophages. Interestingly, FP2 was found to be the predominant population in Las-infected citrus samples while Las-infected psyllids contained primarily FP1. The multiple banding patterns that resulted from amplification of lasAI imply extensive variation exists within the full and partial repeat sequence while the single band from lasAII indicates a low amount of variation within the repeat sequence. Phylogenetic analysis of Las-infected samples from 22 provinces in Thailand suggested that the bacterial pathogen may have been introduced to Thailand from China and the Philippines. This is the first report evaluating the genetic variation of a large population of Ca. L. asiaticus infected samples in Thailand using the two effector genes from Las prophage regions.
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Affiliation(s)
- Thamrongjet Puttamuk
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
- U.S. Horticultural Research Laboratory, US Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
| | - Lijuan Zhou
- U.S. Horticultural Research Laboratory, US Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
| | - Niphone Thaveechai
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Shouan Zhang
- Tropical Research and Education Center, University of Florida, Homestead, Florida, United States of America
| | - Cheryl M. Armstrong
- U.S. Horticultural Research Laboratory, US Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
| | - Yongping Duan
- U.S. Horticultural Research Laboratory, US Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
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Ma W, Liang M, Guan L, Xu M, Wen X, Deng X, Chen J. Population Structures of 'Candidatus Liberibacter asiaticus' in Southern China. PHYTOPATHOLOGY 2014; 104:158-162. [PMID: 24093922 DOI: 10.1094/phyto-04-13-0110-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Huanglongbing (HLB) is a highly detrimental citrus disease associated with 'Candidatus Liberibacter asiaticus', a nonculturable alpha-proteobacterium. Characterization of the bacterial populations is important for development of disease management strategies. In this study, the 'Ca. L. asiaticus' populations in eight provinces in southern China where HLB is endemic were analyzed based on tandem repeat number (TRN) variations in a previously characterized genomic locus CLIBASIA_01645. Of the 224 HLB samples collected, 175 (78.3%) samples yielded single polymerase chain reaction (PCR) amplicons (the single amplicon group, SAG) and 49 (21.7%) samples produced multiple PCR amplicons (the multiple amplicon group, MAG). Variations in SAG are summarized by Nei's diversity index (H) and ratio of TRN ≤ 10/TRN > 10 genotypes (R10). Variations in the MAG are described by the percentage of occurrence (PMAG). At an orchard-level comparison, the 'Ca. L. asiaticus' population from a Guangdong orchard (n = 24) showed H = 0.50, R10 = 23, and PMAG = 0, significantly different from that of the non-Guangdong orchards in Yunnan (n = 23), H = 0.83, R10 = 2.3, and PMAG = 11.5, and in Hainan (n = 35), H = 0.88, R10 = 1.5, and PMAG = 16.7. In a region-level consideration, the Guangdong 'Ca. L. asiaticus' population (n = 78) was H = 0.77, R10 = 25, and PMAG = 1.3, whereas the non-Guangdong population (n = 84) was H = 0.91, R10 = 1.6, and PMAG = 26.9. Overall, significant differences were observed between the 'Ca. L. asiaticus' population from Guangdong Province and those from the other provinces. A strong aggregation of TRN = 6, 7, and 8 genotypes is characteristic to the 'Ca. L. asiaticus' population in Guangdong. Referenced to genome annotation, we propose that rearrangement of tandem repeats at locus CLIBASIA_01645 could be associated with bacterial environmental adaptation.
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Zhou L, Powell CA, Li W, Irey M, Duan Y. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing. PLoS One 2013; 8:e82248. [PMID: 24349235 PMCID: PMC3862640 DOI: 10.1371/journal.pone.0082248] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/22/2013] [Indexed: 01/21/2023] Open
Abstract
Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.
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Affiliation(s)
- Lijuan Zhou
- Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida, United States of America
- Indian River Research and Education Center, University of Florida, Fort Pierce, Florida, United States of America
| | - Charles A. Powell
- Indian River Research and Education Center, University of Florida, Fort Pierce, Florida, United States of America
| | - Wenbin Li
- Center for Plant Health, Science and Technology, Animal and Plant health Inspection Service, US Department of Agriculture, Beltsville, Maryland, United States of America
| | - Mike Irey
- Southern Garden Citrus, U. S. Sugar Corp., Clewiston, Florida, United States of America
| | - Yongping Duan
- Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida, United States of America
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14
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Wang X, Tan J, Bai Z, Su H, Deng X, Li Z, Zhou C, Chen J. Detection and characterization of miniature inverted-repeat transposable elements in “Candidatus Liberibacter asiaticus”. J Bacteriol 2013; 195:3979-86. [PMID: 23813735 PMCID: PMC3754606 DOI: 10.1128/jb.00413-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/25/2013] [Indexed: 02/02/2023] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are nonautonomous transposons (devoid of the transposase gene tps) that affect gene functions through insertion/deletion events. No transposon has yet been reported to occur in “Candidatus Liberibacter asiaticus,” an alphaproteobacterium associated with citrus Huanglongbing (HLB, yellow shoot disease). In this study, two MITEs, MCLas-A and MCLas-B, in “Ca. Liberibacter asiaticus” were detected, and the genome was characterized using 326 isolates collected in China and Florida. MCLas-A had three variants, ranging from 237 to 325 bp, and was inserted into a TTTAGG site of a prophage region. MCLas-A had a pair of 54-bp terminal inverted repeats (TIRs), which contained three tandem repeats of TGGTAACCAC. Both “filled” (with MITE) and “empty” (without MITE) states were detected, suggesting the MITE mobility. The empty sites of all bacterial isolates had TIR tandem repeat remnants (TRR). Frequencies of TRR types varied according to geographical origins. MCLas-B had four variants, ranging from 238 to 250 bp, and was inserted into a TA site of another “Ca. Liberibacter” prophage. The MITE, MCLas-B, had a pair of 23-bp TIRs containing no tandem repeats. No evidence of MCLas-B mobility was found. An identical open reading frame was found upstream of MCLas-A (229 bp) and MCLas-B (232 bp) and was predicted to be a putative tps, suggesting an in cis tps-MITE configuration. MCLas-A and MCLas-B were predominantly copresent in Florida isolates, whereas MCLas-A alone or MCLas-B alone was found in Chinese isolates.
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Affiliation(s)
- Xuefeng Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, People's Republic of China
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Services, U.S. Department of Agriculture, Parlier, California, USA
| | - Jin Tan
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, People's Republic of China
- College of Plant Protection, Southwest University, Chongqing, People's Republic of China
| | - Ziqin Bai
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, People's Republic of China
- College of Plant Protection, Southwest University, Chongqing, People's Republic of China
| | - Huanan Su
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, People's Republic of China
- College of Plant Protection, Southwest University, Chongqing, People's Republic of China
| | - Xiaoling Deng
- Citrus Huanglongbing Research Center, South China Agricultural University, Guangzhou, People's Republic of China
| | - Zhongan Li
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, People's Republic of China
| | - Changyong Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, People's Republic of China
| | - Jianchi Chen
- San Joaquin Valley Agricultural Sciences Center, Agricultural Research Services, U.S. Department of Agriculture, Parlier, California, USA
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Wang N, Trivedi P. Citrus huanglongbing: a newly relevant disease presents unprecedented challenges. PHYTOPATHOLOGY 2013; 103:652-65. [PMID: 23441969 DOI: 10.1094/phyto-12-12-0331-rvw] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Citrus huanglongbing (HLB) is one of the oldest citrus diseases and has been known for over a century. HLB is caused by 'Candidatus Liberibacter' spp. that are phloem-limited, fastidious α-proteobacteria and infect hosts in different Kingdoms (i.e., Animalia and Plantae). When compared with well-characterized, cultivatable plant-pathogenic Gram-negative bacteria, the interactions of uncultured insect-vectored plant-pathogenic bacteria, including 'Ca. Liberibacter' spp., with their hosts remain poorly understood. 'Ca. Liberibacter' spp. have been known to cause HLB, which has been rapidly spreading worldwide, resulting in dramatic economic losses. HLB presents an unprecedented challenge to citrus production. In this review, we focus on the most recent research on citrus, 'Candidatus Liberibacter asiaticus', and psyllid interactions, specifically considering the following topics: evolutionary relationships among 'Ca. Liberibacter' spp., genetic diversity, host range, genome analysis, transmission, virulence mechanisms, and the ecological importance of HLB. Currently, no efficient management strategy is available to control HLB, although some promising progress has been made. Further studies are needed to understand citrus, 'Ca. L. asiaticus', and psyllid interactions to design innovative management strategies. Although HLB has been problematic for over a century, we can only win the battle against HLB with a coordinated and deliberate effort by the citrus industry, citrus growers, researchers, legislatures, and governments.
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Affiliation(s)
- Nian Wang
- Cirtrus Research Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred 33850, USA.
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