About this Dataset

Data From: Multilocus Microsatellite Analysis Of 'Candidatus Liberibacter Asiaticus' Associated With Citrus Huanglongbing Worldwide

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', 'C a. Liberibacter africanus' or 'C a. 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.
Organization: Department of Agriculture
Last updated: 2024-03-30T11:21:32.449622
Tags: ars, data-gov, hlb, huanglongbing

Tables

Huanglongbing Cln-Corrected-Data

@usgov.usda_gov_data_from_multilocus_microsatellite_analysis__2e879576.huanglongbing_cln_corrected_data

15.39 kB
201 rows
18 columns

CREATE TABLE huanglongbing_cln_corrected_data (
  "sample_id" VARCHAR,
  "sampling_location" VARCHAR,
  "sample_date" VARCHAR,
  "genotype" DOUBLE,
  "locusa" DOUBLE,
  "locusb" DOUBLE,
  "locusc" DOUBLE,
  "locusd" DOUBLE,
  "locuse" DOUBLE,
  "locusf" DOUBLE,
  "locusg" DOUBLE,
  "unnamed_11" VARCHAR  -- Unnamed: 11,
  "unnamed_12" VARCHAR  -- Unnamed: 12,
  "unnamed_13" VARCHAR  -- Unnamed: 13,
  "unnamed_14" VARCHAR  -- Unnamed: 14,
  "unnamed_15" VARCHAR  -- Unnamed: 15,
  "unnamed_16" VARCHAR  -- Unnamed: 16,
  "unnamed_17" VARCHAR  -- Unnamed: 17
);

Huanglongbing GT-Populationwise

@usgov.usda_gov_data_from_multilocus_microsatellite_analysis__2e879576.huanglongbing_gt_populationwise

16.82 kB
326 rows
19 columns

CREATE TABLE huanglongbing_gt_populationwise (
  "sample_id" VARCHAR,
  "sampling_location" VARCHAR,
  "sample_date" VARCHAR,
  "genotype" DOUBLE,
  "loucsa" DOUBLE,
  "locusb" DOUBLE,
  "locusc" DOUBLE,
  "locusd" DOUBLE,
  "locuse" DOUBLE,
  "locusf" DOUBLE,
  "locusg" DOUBLE,
  "unnamed_11" VARCHAR  -- Unnamed: 11,
  "unnamed_12" VARCHAR  -- Unnamed: 12,
  "unnamed_13" VARCHAR  -- Unnamed: 13,
  "unnamed_14" VARCHAR  -- Unnamed: 14,
  "unnamed_15" VARCHAR  -- Unnamed: 15,
  "unnamed_16" VARCHAR  -- Unnamed: 16,
  "unnamed_17" VARCHAR  -- Unnamed: 17,
  "unnamed_18" VARCHAR  -- Unnamed: 18
);

Huanglongbing Las-SSR-Genotype

@usgov.usda_gov_data_from_multilocus_microsatellite_analysis__2e879576.huanglongbing_las_ssr_genotype

16.88 kB
326 rows
19 columns

CREATE TABLE huanglongbing_las_ssr_genotype (
  "sample_id" VARCHAR,
  "sampling_location" VARCHAR,
  "sample_date" VARCHAR,
  "genotype" DOUBLE,
  "loucsa" DOUBLE,
  "locusb" DOUBLE,
  "locusc" DOUBLE,
  "locusd" DOUBLE,
  "locuse" DOUBLE,
  "locusf" DOUBLE,
  "locusg" DOUBLE,
  "unnamed_11" VARCHAR  -- Unnamed: 11,
  "unnamed_12" VARCHAR  -- Unnamed: 12,
  "unnamed_13" VARCHAR  -- Unnamed: 13,
  "unnamed_14" VARCHAR  -- Unnamed: 14,
  "unnamed_15" VARCHAR  -- Unnamed: 15,
  "unnamed_16" VARCHAR  -- Unnamed: 16,
  "unnamed_17" VARCHAR  -- Unnamed: 17,
  "unnamed_18" VARCHAR  -- Unnamed: 18
);