Differentiation of Indian,East Timorese,Papuan and Floridian ‘Candidatus Liberibacter asiaticus’ isolates on the basis of simple sequence repeat and single nucleotide polymorphism profiles at 25 loci |
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| Authors: | H Katoh R Davis MW Smith M Weinert T Iwanami |
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| Institution: | 1. National Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), , Tsukuba, Ibaraki, Japan;2. Northern Australia Quarantine Strategy, Australian Quarantine and Inspection Service, Cairns International Airport, , Cairns, QLD, Australia;3. Bundaberg Research Station, Department of Employment, Economic Development and Innovation, , Bundaberg, QLD, Australia;4. Centre for Tropical Agriculture, Department of Employment, Economic Development and Innovation, , Mareeba, QLD, Australia |
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| 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. |
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| Keywords: | ‘ Candidatus Liberibacter asiaticus’ citrus genetic diversity simple sequence repeats |
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