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Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide.

Islam MS, Glynn JM, Bai Y, Duan YP, Coletta-Filho HD, Kuruba G, Civerolo EL, Lin H - BMC Microbiol. (2012)

Bottom Line: HLB-associated Liberibacters have spread to North America and South America in recent years.Our results identified three major genetic groups of 'Ca.L. asiaticus'.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA-ARS San Joaquin Valley Agricultural Research Science Center, Parlier, CA 93648, USA.

ABSTRACT

Background: Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed.

Results: A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide.

Conclusions: Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources of the dominant 'Ca. L. asiaticus' in Florida were not clearly understood, the less-pervasive groups may have been introduced directly from Asia or via Brazil. Notably, the recent outbreak of HLB in Florida probably occurred through multiple introductions. Microsatellite markers developed in this study provide adequate discriminatory power for the identification and differentiation of closely-related isolates, as well as for genetic studies of 'Ca. L. asiaticus'.

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Individual assignments of 'Candidatus Liberibacter asiaticus' isolates obtained from nine different countries from Asia and Americas by STRUCTURE analysis. There were three clusters (K). Black lines within the squares distinguish geographic locations.
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Figure 2: Individual assignments of 'Candidatus Liberibacter asiaticus' isolates obtained from nine different countries from Asia and Americas by STRUCTURE analysis. There were three clusters (K). Black lines within the squares distinguish geographic locations.

Mentions: The STRUCTURE analysis based on Bayesian modeling further assessed the genetic structure of 'Ca. L. asiaticus'. This approach utilizes statistical methods to determine the relationships among the isolates without prior population information. In the analysis three different clusters (K) were identified based on the ad hoc statistic ΔK [23] (Figure 2). The membership of each individual isolate obtained from STRUCTURE analysis, can be estimated as (q), the ancestry coefficient, which varies on a scale between 0-1.0, with 1.0 indicating full membership in a population. Individuals can be assigned to multiple clusters (with values of q summing to 1.0) indicating they are admixed. Individual samples with q ≥ 0.90 (ancestry coefficient) were considered as having single lineage and individuals with q < 0.90 were considered as admixed lineages as followed by Williams et al. [24]. The result of STRUCTURE analysis is consistent with UPGMA in which isolates from India were grouped in a distinct cluster (Figure 2 in yellow). Brazilian and most east-southeast Asian isolates were clustered as a single lineage (q ≥ 0.90) (Figure 2, red). Some isolates taken from central Florida (Polk, Pasco, and Lake Counties) shared the same lineage with east-southeast Asian and Brazilian isolates (Figure 2, red). Most Florida isolates, however, grouped in a different cluster (Figure 2, green). Some admixed isolates (q <0.90) were found in Florida as well as in Baise and Nanning of Guangxi province in China, and in Cambodia.


Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide.

Islam MS, Glynn JM, Bai Y, Duan YP, Coletta-Filho HD, Kuruba G, Civerolo EL, Lin H - BMC Microbiol. (2012)

Individual assignments of 'Candidatus Liberibacter asiaticus' isolates obtained from nine different countries from Asia and Americas by STRUCTURE analysis. There were three clusters (K). Black lines within the squares distinguish geographic locations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368738&req=5

Figure 2: Individual assignments of 'Candidatus Liberibacter asiaticus' isolates obtained from nine different countries from Asia and Americas by STRUCTURE analysis. There were three clusters (K). Black lines within the squares distinguish geographic locations.
Mentions: The STRUCTURE analysis based on Bayesian modeling further assessed the genetic structure of 'Ca. L. asiaticus'. This approach utilizes statistical methods to determine the relationships among the isolates without prior population information. In the analysis three different clusters (K) were identified based on the ad hoc statistic ΔK [23] (Figure 2). The membership of each individual isolate obtained from STRUCTURE analysis, can be estimated as (q), the ancestry coefficient, which varies on a scale between 0-1.0, with 1.0 indicating full membership in a population. Individuals can be assigned to multiple clusters (with values of q summing to 1.0) indicating they are admixed. Individual samples with q ≥ 0.90 (ancestry coefficient) were considered as having single lineage and individuals with q < 0.90 were considered as admixed lineages as followed by Williams et al. [24]. The result of STRUCTURE analysis is consistent with UPGMA in which isolates from India were grouped in a distinct cluster (Figure 2 in yellow). Brazilian and most east-southeast Asian isolates were clustered as a single lineage (q ≥ 0.90) (Figure 2, red). Some isolates taken from central Florida (Polk, Pasco, and Lake Counties) shared the same lineage with east-southeast Asian and Brazilian isolates (Figure 2, red). Most Florida isolates, however, grouped in a different cluster (Figure 2, green). Some admixed isolates (q <0.90) were found in Florida as well as in Baise and Nanning of Guangxi province in China, and in Cambodia.

Bottom Line: HLB-associated Liberibacters have spread to North America and South America in recent years.Our results identified three major genetic groups of 'Ca.L. asiaticus'.

View Article: PubMed Central - HTML - PubMed

Affiliation: USDA-ARS San Joaquin Valley Agricultural Research Science Center, Parlier, CA 93648, USA.

ABSTRACT

Background: Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed.

Results: A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide.

Conclusions: Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources of the dominant 'Ca. L. asiaticus' in Florida were not clearly understood, the less-pervasive groups may have been introduced directly from Asia or via Brazil. Notably, the recent outbreak of HLB in Florida probably occurred through multiple introductions. Microsatellite markers developed in this study provide adequate discriminatory power for the identification and differentiation of closely-related isolates, as well as for genetic studies of 'Ca. L. asiaticus'.

Show MeSH
Related in: MedlinePlus