Multilocus sequences confirm the close genetic relationship of four phytoplasmas of peanut witches'‐broom group 16SrII‐A

Li, Yong; Piao, Chun‐gen; Tian, Guozhong; Liu, Zhixin; Guo, Min-wei; Lin, Cai-li; Wang, Xi-zhuo

doi:10.1002/jobm.201300140

Cited by 13 publications

(4 citation statements)

References 35 publications

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“…For phytoplasmas, most of the MLST schemes that have been developed for “ Candidatus Phytoplasma” species or 16S taxonomic groups target rRNAs, housekeeping genes, protein coding genes, and also positively selected genes involved in the interaction with the host (19, 20). A single study following the classical requirement of an MLST scheme that includes at least seven housekeeping genes and targets a small number of samples is currently available (2, 21). Other studies that targeted three to five housekeeping genes have addressed taxonomic or epidemiological questions (22, 23).…”

Section: Introductionmentioning

confidence: 99%

Multilocus Sequence Analysis Reveals Three Distinct Populations of “ Candidatus Phytoplasma palmicola” with a Specific Geographical Distribution on the African Continent

Pilet

Quaicoe

Osagie

et al. 2019

Appl Environ Microbiol

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To sustain epidemiological studies on coconut lethal yellowing disease (CLYD), a devastating disease in Africa caused by a phytoplasma, we developed a multilocus sequence typing (MLST) scheme for “CandidatusPhytoplasma palmicola” based on eight housekeeping genes. At the continental level, eight different sequence types were identified among 132 “CandidatusPhytoplasma palmicola”-infected coconuts collected in Ghana, Nigeria, and Mozambique, where CLYD epidemics are still very active. “CandidatusPhytoplasma palmicola” appeared to be a bacterium that is subject to strong bottlenecks, reducing the fixation of positively selected beneficial mutations into the bacterial population. This phenomenon, as well as a limited plant host range, might explain the observed country-specific distribution of the eight haplotypes. As an alternative means to increase fitness, bacteria can also undergo genetic exchange; however, no evidence for such recombination events was found for “CandidatusPhytoplasma palmicola.” The implications for CLYD epidemiology and prophylactic control are discussed. The usefulness of seven housekeeping genes to investigate the genetic diversity in the genus “CandidatusPhytoplasma” is underlined.IMPORTANCECoconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme (MLST) for tracking epidemics of “Ca. Phytoplasma palmicola,” which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of “Ca. Phytoplasma palmicola” with low intrapopulation diversity. The reasons for the observed strong geographic patterns remain to be established but could result from the lethality of CLYD and the dominance of short-distance insect-mediated transmission.

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Section: Introductionmentioning

confidence: 99%

Multilocus Sequence Analysis Reveals Three Distinct Populations of “ Candidatus Phytoplasma palmicola” with a Specific Geographical Distribution on the African Continent

Pilet

Quaicoe

Osagie

et al. 2019

Appl Environ Microbiol

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“…The isolated DNA from 32 weeds and other crop species was amplified in nested PCR with P1/P7 and R16F2n/R16R2 primers and obtained 1800 bp and 1250 bp product respectively. About 32 weeds and other crop species belonging to various families were tested by nested PCR using above two primers and results were furnished in Table 2 Several workers amplified phytoplasmas rDNA sequence in PCR with universal primers using total DNA isolated from phytoplasma infected Portulaca olaracea (Savita et al,2014), Pergularia daemia (Rangaswamy et al, 2011), Celosia argentea (Samuitiene and Navalinskiene., 2006), Parthenium hysterophorus (Raj et al, 2008), Tephrosia purpurea (Yadav et al, 2014), Solanum melongena (Kumar et al, 2012), Solanum lycopersicum (Singh et al, 2012) Sesamum indicum (Khan et al, 2007), Cleome viscosa (Li et al, 2014), Saccharum officinarum (Guar et al, 2008), Capsicum annuum (Khan et al, 2005) and Arachis hypogaea (Li et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

Molecular Characterization of Phytoplasma Associated with Crops, Weeds and Forest Trees in Andhra Pradesh, India

Naik¹,

Reddy²,

Rani³

et al. 2018

Int.J.Curr.Microbiol.App.Sci

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“…MLST has become a classic method for epidemiological investigation, identification, transmission traceability, and genetic evolution analysis of pathogenic microorganisms [ 18 ]. Many MLST studies have also been conducted on the differential diagnosis of phytoplasmas and genetic diversity [ 19 , 20 , 21 , 22 , 23 , 24 , 25 ], such as for Flavescence dorée (FD) phytoplasma [ 26 , 27 , 28 ]. Jernej et al [ 29 ] analyzed the occurrence of ‘ Candidatus Phytoplasma pyri ’ in different orchards in Slovenia, and the results showed that 45 samples from different sources could be divided into eight STs by MLST analysis of secY and aceF .…”

Section: Introductionmentioning

confidence: 99%

Molecular Diversity and Evolutionary Relatedness of Paulownia Witches’-Broom Phytoplasma in Different Geographical Distributions in China

Kong

Lin

et al. 2022

Biology

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To reveal the distribution and transmission pathway of Paulownia witches’-broom (PaWB) disease, which is caused by phytoplasmas related to genetic variation, and the adaptability to the hosts and environments of the pathogenic population in different geographical regions in China, in this study, we used ten housekeeping gene fragments, including rp, fusA, secY, tuf, secA, dnaK, rpoB, pyrG, gyrB, and ipt, for multilocus sequence typing (MLST). A total of 142 PaWB phytoplasma strains were collected from 18 provinces or municipalities. The results showed that the genetic diversity was comparatively higher among the PaWB phytoplasma strains, and substantially different from that of the other 16SrI subgroup strains. The number of gene variation sites for different housekeeping genes in the PaWB phytoplasma strains ranged from 1 to 14 SNPs. Among them, rpoB (1.47%) and dnaK (1.12%) had higher genetic variation, and rp (0.20%) had the least genetic variation. The tuf and rpoB genes showed the fixation of positively selected beneficial mutations in the PaWB phytoplasma populations, and all housekeeping genes except tuf followed the neutral evolutionary model. We found an absence of recombination among PaWB phytoplasma sequence types (STs) for each housekeeping gene except dnaK, and no evidence for such recombination events for concatenated sequences of PaWB phytoplasma strains. The 22 sequence types were identified among the concatenated sequences of seven housekeeping genes (rp, fusA, secY, secA, tuf, dnaK, and rpoB) from 105 representative strains. We analyzed all 22 STs by goeBURST algorithm, forming two clonal complexes (CCs) and three singletons. Among them, ST1, as the primary founder of CC1, had the widest geographical distribution, accounting for 72.38% of all strains, with a high frequency of shared sequence type. The results of phylogenetic analysis of the concatenated sequences further revealed that the 105 strains were clustered into two representative lineages of PaWB phytoplasma, with obvious geographical differentiation. The ST1 strains of highly homogeneous lineage-1 were a widespread and predominant population in diseased areas. Lineage-2 contained strains from Jiangxi, Fujian, and Shaanxi provinces, highlighting the close genetic relatedness of the strains in these regions, which was also consistent with the results of most single-gene phylogenetic analysis of each gene. We also found that the variability in the northwest China population was higher than in other geographical populations; the range of genetic differentiation between the south of the Yangtze River population and the Huang-huai-hai Plain (or southwest China) population was relatively large. The achieved diversity and evolution data, as well as the MLST technique, are helpful for epidemiological studies and guiding PaWB disease control decisions.

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Multilocus sequences confirm the close genetic relationship of four phytoplasmas of peanut witches'‐broom group 16SrII‐A

Cited by 13 publications

References 35 publications

Multilocus Sequence Analysis Reveals Three Distinct Populations of “ Candidatus Phytoplasma palmicola” with a Specific Geographical Distribution on the African Continent

Multilocus Sequence Analysis Reveals Three Distinct Populations of “ Candidatus Phytoplasma palmicola” with a Specific Geographical Distribution on the African Continent

Molecular Characterization of Phytoplasma Associated with Crops, Weeds and Forest Trees in Andhra Pradesh, India

Molecular Diversity and Evolutionary Relatedness of Paulownia Witches’-Broom Phytoplasma in Different Geographical Distributions in China

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