scholarly journals A Type 3 Prophage of ‘Candidatus Liberibacter asiaticus’ Carrying a Restriction-Modification System

2018 ◽  
Vol 108 (4) ◽  
pp. 454-461 ◽  
Author(s):  
Zheng Zheng ◽  
Minli Bao ◽  
Fengnian Wu ◽  
Christopher Van Horn ◽  
Jianchi Chen ◽  
...  
Keyword(s):  
Southern China ◽  
Lytic Cycle ◽  
Candidatus Liberibacter Asiaticus ◽  
Specific Pcr ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Type 3 ◽  
Restriction Modification

Prophages, the lysogenic form of bacterial phages, are important genetic entities of ‘Candidatus Liberibacter asiaticus’ (CLas), a nonculturable α-proteobacterium associated with citrus Huanglongbing. Two CLas prophages have been described, SC1 (NC_019549.1, Type 1) and SC2 (NC_019550.1, Type 2), which involve the lytic cycle and the lysogenic cycle, respectively. To explore the prophage repertoire, 523 CLas DNA samples extracted from leaf petioles of CLas-infected citrus were collected from southern China and surveyed for Type 1 and Type 2 prophages by specific PCR. Eighteen samples were found lacking both prophages. One sample, JXGC, sequenced using Illumina HiSeq, generated >100 million short sequence reads (150 bp per read). Read mapping to known prophage sequences showed a sequence coverage of 46% to SC1 and 50% to SC2. BLAST search using SC1 and SC2 as queries identified three contigs from the JXGC de novo assembly that form a circular P-JXGC-3 (31,449 bp), designated as a new Type 3 prophage. Chromosomal integration of P-JXGC-3 was detected to occur within a helicase gene, resulting in a duplication of this gene. P-JXGC-3 had 36 open reading frames (ORFs), 10 of which were not found in Type 1 or Type 2 prophages, including four genes that encoded a restriction-modification (R-M) system (hsdR, hsdS, hsdM1, and hsdM2). Typed by prophage-specific PCR, the CLas strains in southern China contained all combinations of the three prophage types with the exception of a Type 2−Type 3 combination, suggesting active ongoing prophage−phage interactions. Based on gene annotation, P-JXGC-3 is not capable of reproduction via the lytic cycle. The R-M system was speculated to play a role against Type 1 prophage−phage invasion.

scholarly journals Investigation of Citrus HLB Symptom Variations Associated with “Candidatus Liberibacter asiaticus” Strains Harboring Different Phages in Southern China

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2262
Author(s):  
Minli Bao ◽  
Zheng Zheng ◽  
Jianchi Chen ◽  
Xiaoling Deng
Keyword(s):  
Southern China ◽  
Phage Type ◽  
Genomic Research ◽  
Citrus Limon ◽  
Symptom Development ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

Huanglongbing (HLB) is a devastating disease affecting citrus production worldwide. In China, the disease is associated with an unculturable alpha-proteobacterium, “Candidatus Liberibacter asiaticus” (CLas). Phages/prophages of CLas have recently been identified through intensive genomic research. The phage information has facilitated research on CLas biology such as population diversity and virulence gene identification. However, little is known about the roles of CLas phages in HLB symptom development. Such research is challenging due to the unculturable nature of CLas and the lack of laboratory strains that carry a single phage. In this study, CLas strains singly carrying Type 1 phage (Type 1 CLas) and Type 2 phage (Type 2 CLas) were identified and maintained in an experimental screenhouse in southern China. The strains were characterized through next-generation sequencing (NGS). Then, each CLas strain was inoculated into seedlings of three different citrus cultivars/species through graft transmission in a screenhouse in Guangdong, China. Symptom developments were recorded. All CLas-infected cultivars showed HLB symptoms in seven months. In cultivar Nianju (Citrus reticulata), Type 1 CLas caused pronounced yellowing symptoms and severe defoliation, whereas Type 2 CLas caused typical Zn-deficiency-like symptoms. In contrast, symptoms from the two CLas strains’ infections on cultivars Shatianyu (C. maxima), and Eureka lemon (Citrus limon) were more difficult to differentiate. Results from this study provide baseline information for future research to investigate the roles of CLas phages in HLB symptom development.

scholarly journals Two ‘Candidatus Liberibacter asiaticus’ Strains Recently Found in California Harbor Different Prophages

2017 ◽  
Vol 107 (6) ◽  
pp. 662-668 ◽  
Author(s):  
Z. Zheng ◽  
F. Wu ◽  
L. B. Kumagai ◽  
M. Polek ◽  
X. Deng ◽  
...  
Keyword(s):  
Los Angeles ◽  
Geographic Region ◽  
Mapping Technique ◽  
Polymorphism Analysis ◽  
Candidatus Liberibacter Asiaticus ◽  
Next Generation Sequencing Technology ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

‘Candidatus Liberibacter asiaticus’ (CLas), an α-proteobacterium, is associated with citrus Huanglongbing (HLB; yellow shoot disease). In California, two cases of CLas have been detected in Los Angeles County, one in Hacienda Heights in 2012 and the other in San Gabriel in 2015. Although all infected trees were destroyed in compliance with a state mandate, citrus industry stakeholder concerns about HLB in California are high. Little is known about the biology of CLas, particularly the California strains, hindering effective HLB management efforts. In this study, next-generation sequencing technology (Illumina MiSeq) was employed to characterize the California CLas strains. Data sets containing >4 billion (Giga) bp of sequence were generated from each CLas sample. Two prophages (P-HHCA1-2 and P-SGCA5-1) were identified by the MiSeq read mapping technique referenced to two known Florida CLas prophage sequences, SC1 and SC2. P-HHCA1-2 was an SC2-like or Type 2 prophage of 38,989 bp in size. P-SGCA5-1 was an SC1-like or Type 1 prophage of 37,487 bp in size. Phylogenetic analysis revealed that P-HHCA1-2 was part of an Asiatic lineage within the Type 2 prophage group. Similarly, P-SGCA5-1 was part of an Asiatic lineage within Type 1 prophage group. The Asiatic relatedness of both P-HHCA1-2 and P-SGCA5-1 was further presented by single nucleotide polymorphism analysis at terL (encoding prophage terminase) that has been established for CLas strain differentiation. The presence of different prophages suggests that the two California CLas strains could have been introduced from different sources. An alternative explanation is that there was a mixed CLas population containing the two types of prophages, and limited sampling in a geographic region may not accurately depict the true CLas diversity. More accurate pathway analysis may be achieved by including more strains collected from the regions.

scholarly journals Prophage Diversity of ‘Candidatus Liberibacter asiaticus’ Strains in California

2019 ◽  
Vol 109 (4) ◽  
pp. 551-559 ◽  
Author(s):  
Z. Dai ◽  
F. Wu ◽  
Z. Zheng ◽  
R. Yokomi ◽  
L. Kumagai ◽  
...  
Keyword(s):  
Los Angeles ◽  
Draft Genome ◽  
Illumina Miseq ◽  
The United States ◽  
Genomic Diversity ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

Huanglongbing (HLB) is a highly destructive citrus disease and is associated with a nonculturable bacterium, ‘Candidatus Liberibacter asiaticus’. ‘Ca. L. asiaticus’ in the United States was first found in Florida in 2005 and is now endemic there. In California, ‘Ca. L. asiaticus’ was first detected in Hacienda Heights in Los Angeles County in 2012 and has now been detected in multiple urban locations in southern California. Knowledge of ‘Ca. L. asiaticus’ strain diversity in California is important for HLB management. In this study, genomic diversity among 10 ‘Ca. L. asiaticus’ strains from six California locations were analyzed using a next-generation sequencing (NGS) (Illumina MiSeq and HiSeq) approach. Draft genome sequences of ‘Ca. L. asiaticus’ strains were assembled. Sequences of the 16S ribosomal RNA gene and nrdB confirmed ‘Ca. L. asiaticus’ identity. Prophages were detected in all ‘Ca. L. asiaticus’ strains. The California ‘Ca. L. asiaticus’ strains formed four prophage typing groups (PTGs): PTG1, with type 1 prophage only (strains from Anaheim, San Gabriel, and Riverside); PTG2, with type 2 prophage only (strains from Hacienda Heights); PTG1-3, with both type 1 and 3 prophages (a strain from Cerritos); and PTG1-2, with both type 1 and type 2 prophages (a strain from La Habra). Analyses of the terL sequence showed that all California ‘Ca. L. asiaticus’ strains were not introduced from Florida but likely from locations in Asia. Miniature inverted-repeat transposable elements were found in all ‘Ca. L. asiaticus’ strains, yet, a jumping-out event was detected in the ‘Ca. L. asiaticus’ strain from Cerritos. Altogether, this study demonstrated that the NGS approach focusing on prophage variation was sensitive and effective in revealing diversity of ‘Ca. L. asiaticus’ strains in California.

scholarly journals 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

2018 ◽  
Vol 108 (11) ◽  
pp. 1224-1236 ◽  
Author(s):  
Zheng Zheng ◽  
Jianchi Chen ◽  
Xiaoling Deng
Keyword(s):  
Southern China ◽  
Candidatus Liberibacter Asiaticus ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Historical Perspectives ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Huanglongbing ◽  
Liberibacter Asiaticus ◽  
Generation Sequencing

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.

Detection of Candidatus Liberibacter asiaticus from Wampee (Clausena lansium Skeels) by Nested PCR

2007 ◽  
Vol 8 (1) ◽  
pp. 53 ◽  
Author(s):  
Xiaoling Deng ◽  
Gen Zhou ◽  
Huaping Li ◽  
Jianchi Chen ◽  
Edwin L. Civerolo
Keyword(s):  
Nested Pcr ◽  
Southern China ◽  
Diaphorina Citri ◽  
Candidatus Liberibacter Asiaticus ◽  
Term Survival ◽  
Disease Vector ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Citrus Orchards

Wampee (Clausena lansium Skeels) is native to southern China and Southeast Asia. Wampee trees are attractive, with grape-like fruits and a muscat taste and are popular in home gardens. Like other members of Rutaceae, wampee has long been suspected to have yellow shoot disease or Huanglongbing (HLB) and Diaphorina citri, the disease vector, was capable of a long-term survival on Wampee. The authors recommend that eradication of wampee trees surrounding citrus orchards should be part of the overall management of citrus HLB. Accepted for publication 20 December 2007. Published 19 April 2007.

scholarly journals Genome Sequence Resource of “Candidatus Liberibacter asiaticus” strain Myan16 from Myanmar

Plant Disease ◽  
2020 ◽  
Author(s):  
Yongqin Zheng ◽  
jun guo ◽  
Xiaoling Deng ◽  
Zheng Zheng
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Sequence Database ◽  
Candidatus Liberibacter Asiaticus ◽  
Genome Sequence Database ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Huanglongbing ◽  
Liberibacter Asiaticus

“Candidatus Liberibacter asiaticus” (CaLas), an uncultured α-proteobacterium, is associated with citrus Huanglongbing (HLB, yellow shoot disease), a destructive disease threatening citrus production worldwide. Here, we reported the draft genome sequence of CaLas strain Myan16 from a HLB-affected lime tree in Myitkyina, Kachin State, Myanmar. The strain Myan16 genome is 1,229,102 bp with an average G+C content of 36.4%, along with a circular prophage: P-Myan16-2 (36,303 bp, Type 2). This is the first genome sequence of CaLas strain from Myanmar, which will enrich the current CaLas genome sequence database and facilitate HLB epidemiology research in Asia and world.

scholarly journals Genome Sequence Resources of Two ‘Candidatus Liberibacter asiaticus’ Strains from Pakistan

Plant Disease ◽  
2020 ◽  
Vol 104 (8) ◽  
pp. 2048-2050 ◽  
Author(s):  
Kehong Liu ◽  
Sagheer Atta ◽  
Xuejin Cui ◽  
Chunhua Zeng ◽  
Jianchi Chen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gc Content ◽  
Sequence Database ◽  
Candidatus Liberibacter Asiaticus ◽  
Genome Sequences ◽  
Citrus Production ◽  
Candidatus Liberibacter ◽  
Citrus Huanglongbing ◽  
Liberibacter Asiaticus

‘Candidatus Liberibacter asiaticus’ (CLas) is an unculturable, phloem-restricted αProteobacteria, associated with citrus Huanglongbing (HLB), which is one of the most destructive diseases in citrus production worldwide. Here, we present the genome sequences of CLas strains PA19 and PA20 from HLB-affected kinnow trees in Multan, Punjab Province, Pakistan. The CLas genomes of PA19 and PA20 comprise 1,224,156 bp and 1,226,225 bp, respectively, with an average GC content of 36.4%. Both harbored the Type 2 prophage. In this study, we report two CLas genomes from Pakistan, which extends the sequence database of CLas and will contribute to CLas biology and HLB management.

The grouping of soils with similar charge properties as a basis for agrotechnology transfer

Soil Research ◽  
1987 ◽  
Vol 25 (3) ◽  
pp. 275 ◽  
Author(s):  
GP Gillman ◽  
DF Sinclair
Keyword(s):  
Cation Exchange ◽  
Cation Exchange Capacity ◽  
Southern China ◽  
Exchange Capacity ◽  
Eastern United States ◽  
Anion Exchange Capacity ◽  
Basic Cation ◽  
Type 3

A set of 94 variable charge soils (Oxisols and Ultisols) from humid tropical Queensland has been formed into three groups on the basis of their surface charge characteristics. Mean curves of basic cation exchange capacity (CECB) against pH, total cation exchange capacity (CECT) against pH, and anion exchange capacity (AEC) against pH for each group at various soil depths were derived, to describe the essential features of each group, designated as Type 1, Type 2 and Type 3 soils. Type 1 soils have high CEC and low AEC, Type 2 soils have low CEC and low AEC, and Type 3 soils have low CEC and high AEC. A number of statistical devices were employed to illustrate the clear separation of the three groups. Additional Oxisol and Ultisol soils from southern China, Peru and the south-eastern United States were successfully allocated to our three groups, but this was not possible for some Andisols from Papua New Guinea. Aspects of possible different management requirements of each group are discussed.

scholarly journals Acid Soil Improvement Enhances Disease Tolerance in Citrus Infected by Candidatus Liberibacter asiaticus

2020 ◽  
Vol 21 (10) ◽  
pp. 3614
Author(s):  
Bo Li ◽  
Shuangchao Wang ◽  
Yi Zhang ◽  
Dewen Qiu
Keyword(s):  
Soil Ph ◽  
Southern China ◽  
Acid Soil ◽  
Sieve Tube ◽  
Soil Improvement ◽  
Economic Losses ◽  
Endurance Capacity ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

Huanglongbing (HLB) is a devastating citrus disease that has caused massive economic losses to the citrus industry worldwide. The disease is endemic in most citrus-producing areas of southern China, especially in the sweet orange orchards where soil acidification has intensified. In this work, we used lime as soil pH amendment to optimize soil pH and enhance the endurance capacity of citrus against Candidatus Liberibacter asiaticus (CLas). The results showed that regulation of soil acidity is effective to reduce the occurrence of new infections and mitigate disease severity in the presence of HLB disease. We also studied the associated molecular mechanism and found that acid soil improvement can (i) increase the root metabolic activity and up-regulate the expression of ion transporter-related genes in HLB-infected roots, (ii) alleviate the physiological disorders of sieve tube blockage of HLB-infected leaves, (iii) strengthen the citrus immune response by increasing the expression of genes involved in SAR and activating the salicylic acid signal pathway, (iv) up-regulate 55 proteins related to stress/defence response and secondary metabolism. This study contributes to a better understanding of the correlation between environment factors and HLB disease outbreaks and also suggests that acid soil improvement is of potential value for the management of HLB disease in southern China.

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