scholarly journals Evaluation of Genetic Diversity Among ‘Candidatus Liberibacter asiaticus’ Isolates Collected in Southeast Asia

2009 ◽  
Vol 99 (9) ◽  
pp. 1062-1069 ◽  
Author(s):  
Kenta Tomimura ◽  
Shin-ichi Miyata ◽  
Noriko Furuya ◽  
Kenji Kubota ◽  
Mitsuru Okuda ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southeast Asia ◽  
Gene Cluster ◽  
Dna Polymerase ◽  
Intergenic Spacer ◽  
Southeast Asian ◽  
Candidatus Liberibacter Asiaticus ◽  
Nucleotide Substitutions ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

The aim of this study was to investigate the genetic diversity and relationships among ‘Candidatus Liberibacter asiaticus’ isolates from different hosts and distinct geographical areas in Southeast Asia. Genetic diversity among ‘Ca. Liberibacter asiaticus’ was estimated by sequencing four well-characterized DNA fragments: the 16S ribosomal DNA (rDNA) and 16S/23S intergenic spacer regions; the outer membrane protein (omp) gene region; the trmU-tufB-secE-nusG-rplKAJL-rpoB region (gene cluster region); and the bacteriophage-type DNA polymerase region. The sequences of the 16S rDNA and 16S/23S intergenic spacer regions were identical among all ‘Ca. Liberibacter asiaticus’ isolates. In contrast, nucleotide substitutions were observed in both the omp gene and the gene cluster regions. However, extended bacteriophage-type DNA polymerase sequences acquired by thermal asymmetric interlaced polymerase chain reaction provided the most sequence diversity among isolates. Phylogenetic analysis of the bacteriophage-type DNA polymerase sequences revealed three clusters in the Southeast Asian ‘Ca. Liberibacter asiaticus’ population. All Indonesian ‘Ca. Liberibacter asiaticus’ isolates clustered in one group. The other clusters were not correlated with geographic distribution. The differences in genetic sequences did not reflect differences in the original citrus host (mandarin or pummelo). These results suggest that the bacteriophage-type DNA polymerase region would be useful for molecular differentiation between different Southeast Asian ‘Ca. Liberibacter asiaticus’ isolates.

scholarly journals Genetic Diversity of Candidatus Liberibacter asiaticus Based on Two Hypervariable Effector Genes in Thailand

PLoS ONE ◽  
2014 ◽  
Vol 9 (12) ◽  
pp. e112968 ◽  
Author(s):  
Thamrongjet Puttamuk ◽  
Lijuan Zhou ◽  
Niphone Thaveechai ◽  
Shouan Zhang ◽  
Cheryl M. Armstrong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidatus Liberibacter Asiaticus ◽  
Effector Genes ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

scholarly journals First Report of the Causal Agent of Huanglongbing (“Candidatus Liberibacter asiaticus”) Infecting Kumquat in Taiwan

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1360-1360 ◽  
Author(s):  
C.-H. Tsai ◽  
H.-J. Su ◽  
Y.-C. Liao ◽  
T.-H. Hung
Keyword(s):  
16S Rrna ◽  
Lateral Roots ◽  
Severe Disease ◽  
Intergenic Spacer ◽  
Sieve Tube ◽  
Causal Agent ◽  
Candidatus Liberibacter Asiaticus ◽  
Intergenic Spacer Region ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

Huanglongbing (greening) disease caused by a nonculturable, phloem-limited bacterium is a severe disease of citrus. On the basis of the influence of temperature on host symptoms and the causal agent, this disease can be categorized as Asian caused by “Candidatus Liberibacter asiaticus”, African caused by “Ca. L. africanus”, and American caused by “Ca. L. americanus”. Kumquat (Fortunella margarita (Lour.) Swingle), a member of the Rutaceae is an economically important crop for export and local consumption in Taiwan. Recently, a Huanglongbing-like disease was found on kumquat in Yilan County, the largest kumquat-producing area in northeastern Taiwan. Even though the disease has been reported on Citrus spp. from Taiwan, it has never been reported on kumquat. Symptoms of infected kumquat were mottling, yellowing, hardening, and curling of leaves followed by premature defoliation, twig dieback, decay of feeder rootlets and lateral roots, and ultimately the death of the entire plant. Typical sieve-tube-restricted bacteria were observed in kumquat cells by electron microscopy (1). In addition, psyllid-transmission tests demonstrated that the Asian psyllid (Diaphorina citri) could transmit this bacterium to healthy kumquats. Positive bud graft transmissions were obtained to F. margarita, F. japonica (Thunb.) Swingle, F. obovata Hort. ex Tanaka, Luchen sweet orange (Citrus sinensis (L.) Osb.), and Wentan pummelo (C. maxima f. sp. butan Hay.). These inoculated plants showed symptoms in 3 to 8 months, and bacteria could be detected by polymerase chain reaction (PCR) using a common primer pair that amplified a 226-bp specific DNA fragment (2). For further molecular identification, the bacterial DNA was extracted from the inoculated plants and PCR was performed by using two sets of primers selected from the 16S rRNA region (GenBank Accession No. L22532) and 16S/23S intergenic spacer region (GenBank Accession No. AB019793). The expected DNA fragments of 1,389 bp and 862 bp were, respectively, amplified from symptomatic plants but not from healthy plants. The PCR products were cloned and sequenced (GenBank Accession Nos. DQ302750 and DQ207841). The 16S rRNA has 98 to 99% identity and 16S/23S intergenic spacer region has 99% identity to the corresponding region of “Ca. L. asiaticus” in GenBank. These molecular analyses confirm the presence of “Ca. L. asiaticus” in kumquat. Since Huanglongbing has been rarely reported naturally on kumquat, further analysis of this bacterium as a special strain of “Ca. L. asiaticus” is needed. References: (1) M. Garnier et al. Ann. Microbiol. 135A:169, 1984. (2) T. H. Hung et al. J. Phytopathol. 147:599, 1999.

Genetic diversity of ‘Candidatus Liberibacter asiaticus’ in Brazil analyzed in different geographic regions and citrus varieties

2019 ◽  
Vol 154 (4) ◽  
pp. 863-872
Author(s):  
Larissa Bonevaes de Paula ◽  
Hong Lin ◽  
Eduardo Sanches Stuchi ◽  
Carolina Sardinha Francisco ◽  
Nágela Gomes Safady ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidatus Liberibacter Asiaticus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Geographic Regions ◽  
Citrus Varieties

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.

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