Differentiation of Indian, East Timorese, Papuan and Floridian ‘CandidatusLiberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci

Abstract

Japanese isolates of ‘Candidatus Liberibacter asiaticus’ have been shown to be clearly differentiated by simple sequence repeat (SSR) profiles at four loci. In this study, 25 SSR loci, including these four loci, were selected from the whole‐genome sequence and were used to differentiate non‐Japanese samples of ‘Ca. Liberibacter asiaticus’ (13 Indian, 3 East Timorese, 1 Papuan and 8 Floridian samples). Out of the 25 SSR loci, 13 were polymorphic. Dendrogram analysis using SSR loci showed that the clusters were mostly consistent with the geographical origins of the isolates. When single nucleotide polymorphisms (SNPs) were searched around these 25 loci, only the upstream region of locus 091 exhibited polymorphism. Phylogenetic tree analysis of the SNPs in the upstream region of locus 091 showed that Floridian samples were clustered into one group as shown by dendrogram analysis using SSR loci. The differences in nucleotide sequences were not associated with differences in the citrus hosts (lime, mandarin, lemon and sour orange) from which the isolates were originally derived.

Changes in Variable Number of Tandem Repeats in ‘Candidatus Liberibacter asiaticus’ through Insect Transmission

“…VNTRs in bacterial DNA have been used as markers for differentiating and subtyping strains of several bacterial species, including ‘ Ca . L. asiaticus’ [ 20 , 21 , 22 ]. In a previous study, Katoh et al [ 21 ] selected four highly polymorphic VNTR loci and these VNTR markers were used to estimate the genetic diversity and population structures of ‘ Ca .…”

“…In a previous study, Katoh et al [ 21 ] selected four highly polymorphic VNTR loci and these VNTR markers were used to estimate the genetic diversity and population structures of ‘ Ca . L. asiaticus’ in Japan, Taiwan, India, Indonesia, Timor-Leste, Papua New Guinea, and Florida [ 21 , 22 ]. Using these VNTR markers at four loci, Matos et al [ 23 ] also performed an extended analysis of ‘ Ca .…”

Validation of ‘Variable Number of Tandem Repeat’-Based Approach for Examination of ‘Candidatus Liberibacter asiaticus’ Diversity and Its Applications for the Analysis of the Pathogen Populations in the Areas of Recent Introduction

“…In addition to these genes, the rplKAJL-rpoBC operon sequence, nusG-rplK , and bacteriophage-type DNA polymerase region [30], [31], [32], [33] have been used for genetic differentiation of C Las. The completion of the C Las genome sequence [34] has allowed identifying different regions of the genome with variable number of tandem repeats (VNTRs) [35], [36], [37], [38], [39]. Such VNTRs also known as microsatellites or short sequence repeats have been found in the genomes of various eukaryotic and prokaryotic organisms and represent tandem repetitive DNA sequences with a motif length of 2 to 6 or more base pairs (bp) [40].…”

“…These data, however, were obtained based on the analysis of a single locus, which may not provide enough information for discrimination between different strains of C Las. More recently, a number of studies conducted by several research groups were published that identified additional loci containing hyper-variable sequence regions in the C Las genome that could be used for differentiating strains of the bacterium [35], [36], [37], [38]. Although these publications demonstrated the potential of VNTR-based approach for examination of C Las variability, an important question that needed to be addressed in order to validate this approach was: how stable are these repeats upon multiplication of the pathogen in a host over an extended period of time and upon its passaging from a host to a host?…”

Diversity and characterization of Candidatus Liberibacter asiaticus strains causing huanglongbing disease in Iran, based on two prophage loci

“…Since the publication of CLas genome sequences, it has been demonstrated that a number of loci such as simple sequence repeat (SSR) and prophage genes are better markers for differentiating CLas isolates from different geographic origins including South-East Asia (Tomimura et al, 2009), China (Chen et al, 2010;Liu et al, 2011), Florida (Chen et al, 2010), Japan, Taiwan and Indonesia (Katoh, Davis, Smith, Weinert, & Iwanami, 2012;Katoh et al, 2011).…”