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Data from: Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide

posted on 2024-02-13, 13:44 authored by Md-Sajedul Islam, Jonathan M. Glynn, Yang Bai, Yong-Ping Duan, Helvecio D. Coletta-Filho, Gopal Kuruba, Edwin L. Civerolo, Hong Lin

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.

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.

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'.

The supporting data provides sample and haplotype information for all isolates used in this study: Huanglongbing_Las-SSR-Genotype; Huanglongbing_GT-Populationwise; and Huanglongbing_Cln-Corrected-Dat.

Resources in this dataset:

  • Resource Title: Data Dictionary.

    File Name: Huanglongbing_DataDictionary.csv

    Resource Description: Defines variables and data types for CSV tables.

  • Resource Title: Las-SSR Genotype.

    File Name: Huanglongbing_Las-SSR-Genotype.csv

    Resource Description: Candidatus Liberibacter asiaticus Simple sequence repeats (SSRs)

  • Resource Title: GT-Populationwise.

    File Name: Huanglongbing_GT-Populationwise.csv

    Resource Description: Gene targeting (GT) population information for isolates.

  • Resource Title: Cln-Corrected-Data.

    File Name: Huanglongbing_Cln-Corrected-Data.csv

    Resource Description: A clone-corrected (removing repeated genotypes within a population) data set built and used for the analysis of genetic diversity, linkage disequilibrium and genetic structure.


USDA-ARS: 5302-22000-008-40T


Data contact name

Lin, Hong

Data contact email


Ag Data Commons

Intended use

To develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection.

Temporal Extent Start Date


Temporal Extent End Date



  • Not specified

Geographic location - description

Florida; Brazil; China; India; Cambodia; Vietnam; Taiwan; Thailand; Japan

ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

greening disease; Citrus; Proteobacteria; Candidatus Liberibacter asiaticus; North America; population structure; nucleotide sequences; genetic markers; bacteria; genetic analysis; United States; Florida; Brazil; China; India; Cambodia; Vietnam; Taiwan; Thailand; Japan; microsatellite repeats; genetic variation; Asia; South America; haplotypes; Plant Science and Plant Products

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Islam, Md-Sajedul; Glynn, Jonathan M.; Bai, Yang; Duan, Yong-Ping; Coletta-Filho, Helvecio D.; Kuruba, Gopal; Civerolo, Edwin L.; Lin, Hong (2019). Data from: Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide. Ag Data Commons.

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