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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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Sample distribution of 'Candidatus Liberibacter asiaticus' from 15 citrus-growing counties (gray highlighted) in Florida, USA. Green circles indicate the counties where only the dominant 'Ca. L. asiaticus' group were observed based on STRUCTURE analysis (green in Figure 2). Some isolates from Polk County (13), Pasco County (14) and Lake County (15) were included with the genetic group 2 (less dominant group) (see Figure 2).
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Figure 4: Sample distribution of 'Candidatus Liberibacter asiaticus' from 15 citrus-growing counties (gray highlighted) in Florida, USA. Green circles indicate the counties where only the dominant 'Ca. L. asiaticus' group were observed based on STRUCTURE analysis (green in Figure 2). Some isolates from Polk County (13), Pasco County (14) and Lake County (15) were included with the genetic group 2 (less dominant group) (see Figure 2).

Mentions: eBURST analysis provided further insights into the origin of 'Ca. L. asiaticus'. Founder haplotypes were identified from China, Brazil, and India. Based on their position within the eBURST network, these founders are predicted to have given rise to the three global genetic groups, consistent with prevailing theories of the geographic origins of HLB [1,2,4,7]. While one founder type was predicted in Brazil, the similar genetic makeup of Brazilian and east-southeast Asian isolates suggest that this founder could have been introduced into Brazil from any of these Asian countries. Consistent with the STRUCTURE analysis, the eBURST diagram also predicted the introduction of 'Ca. L. asiaticus' into Florida citrus groves through at least two separate introduction events. While a primary network was detected between a founder haplotype from China and two unique haplotypes in Florida, clear differentiation was observed between most isolates from China and Florida by Bayesian clustering and UPGMA analyses. Differences between the dominant groups found in Florida and China were also reported in a recent study using a single VNTR locus [21]. It is uncertain whether the dominant group of Florida isolates were introduced en masse or if a small population of nearly-identical 'Ca. L. asiaticus' haplotypes from China were introduced, evolved quickly, and established a large population. The recent discovery and rapid spread of HLB in Florida, along with wide distribution of dominant 'Ca. L. asiaticus' group observed in the present study suggests that isolates of this group have been directly introduced from an unknown location. Another recent study also indicated that some isolates of 'Ca. L. asiaticus' from Florida may have been introduced through two different events, and sources were unknown [21]. The analyses of microsatellites in the present study, however, suggest that the introduction of the less-dominant cluster was likely from a single source either Asia or Brazil. The low occurrence of less dominant group in some central counties in Florida suggests that the members of this group were perhaps introduced more recently (Figure 4). However, it is certainly plausible that these two haplotypes were introduced into Florida at nearly the same time. Isolates from one of the sources may have spread quickly due to selective advantage under a favorable set of biological or environmental conditions.


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)

Sample distribution of 'Candidatus Liberibacter asiaticus' from 15 citrus-growing counties (gray highlighted) in Florida, USA. Green circles indicate the counties where only the dominant 'Ca. L. asiaticus' group were observed based on STRUCTURE analysis (green in Figure 2). Some isolates from Polk County (13), Pasco County (14) and Lake County (15) were included with the genetic group 2 (less dominant group) (see Figure 2).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Sample distribution of 'Candidatus Liberibacter asiaticus' from 15 citrus-growing counties (gray highlighted) in Florida, USA. Green circles indicate the counties where only the dominant 'Ca. L. asiaticus' group were observed based on STRUCTURE analysis (green in Figure 2). Some isolates from Polk County (13), Pasco County (14) and Lake County (15) were included with the genetic group 2 (less dominant group) (see Figure 2).
Mentions: eBURST analysis provided further insights into the origin of 'Ca. L. asiaticus'. Founder haplotypes were identified from China, Brazil, and India. Based on their position within the eBURST network, these founders are predicted to have given rise to the three global genetic groups, consistent with prevailing theories of the geographic origins of HLB [1,2,4,7]. While one founder type was predicted in Brazil, the similar genetic makeup of Brazilian and east-southeast Asian isolates suggest that this founder could have been introduced into Brazil from any of these Asian countries. Consistent with the STRUCTURE analysis, the eBURST diagram also predicted the introduction of 'Ca. L. asiaticus' into Florida citrus groves through at least two separate introduction events. While a primary network was detected between a founder haplotype from China and two unique haplotypes in Florida, clear differentiation was observed between most isolates from China and Florida by Bayesian clustering and UPGMA analyses. Differences between the dominant groups found in Florida and China were also reported in a recent study using a single VNTR locus [21]. It is uncertain whether the dominant group of Florida isolates were introduced en masse or if a small population of nearly-identical 'Ca. L. asiaticus' haplotypes from China were introduced, evolved quickly, and established a large population. The recent discovery and rapid spread of HLB in Florida, along with wide distribution of dominant 'Ca. L. asiaticus' group observed in the present study suggests that isolates of this group have been directly introduced from an unknown location. Another recent study also indicated that some isolates of 'Ca. L. asiaticus' from Florida may have been introduced through two different events, and sources were unknown [21]. The analyses of microsatellites in the present study, however, suggest that the introduction of the less-dominant cluster was likely from a single source either Asia or Brazil. The low occurrence of less dominant group in some central counties in Florida suggests that the members of this group were perhaps introduced more recently (Figure 4). However, it is certainly plausible that these two haplotypes were introduced into Florida at nearly the same time. Isolates from one of the sources may have spread quickly due to selective advantage under a favorable set of biological or environmental conditions.

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