Characterization of “Candidatus Liberibacter Asiaticus” Populations by Double-Locus Analyses

Abstract

"Candidatus Liberibacter asiaticus" (CaLas) is associated with citrus Huanglongbing (HLB, yellow shoot disease), which is highly destructive to world citrus production. Understanding the relationships of CaLas isolates from different geographical regions is important for HLB research and development of disease management strategies. In this study, 301 CaLas isolates [85 Brazil, 132 China, and 84 U.S. (83 Florida and 1 California)] were collected, and genomic variations among them were evaluated based on the analyses of two genomic loci: trn1, characteristic of variable tandem repeat numbers (TRNs), and snp1, characteristic of single nucleotide polymorphisms (SNPs). Locus trn1 revealed the homogeneity of all Brazilian isolates, and locus snp1 revealed the homogeneity of most Florida isolates. When the two loci were analyzed simultaneously, i.e., double-locus (DL) analyses, CaLas isolates were clustered mostly according to geographical origins. DL genotype 1 included 97 % of the Chinese isolates, DL genotype 2 included all Brazilian isolates, and DL genotype 3 included 93 % of the U.S. isolates. DL analyses successfully revealed inter-continental overlapping or movement pattern of CaLas isolates. The isolate recently found in California belonged to Asiatic DL genotype 1.

Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida

“…Unlike the Asiatic origin of CLas strains in California 14 , 28 , Californian ACP was likely of America origin. Therefore, CLas and ACP might have been introduced in two separate events.…”

“…ACP was first detected in southern California (San Diego County) in 2008 13 and continues spreading northward. We have research interests in tracking HLB development in California and demonstrated that the Californian strains of CLas were associated with Asiatic strains but not the Floridian strain 14 . Yet, the possible origin of the Californian ACP has not been studied.…”

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

“…Sequence diversity has been reported in the prophage terminase (CLIBASIA_ 05610) locus, and this diversity was used for genetic differences between Chinese isolates and Florida isolates (Deng et al., ; Liu et al., ); however, none of the SNPs created a termination codon. Interestingly, sequence diversity in this locus in the Iranian strains (F3 and I1) did not create any termination codon and open reading frameshift and showed high identity.…”

“…It has been confirmed that a VTRN in the CLIBASIA _01645 locus of the CLas genome is a good marker for detecting CLas diversity among isolates from different countries (Chen et al., ; Katoh et al., ). Subsequently, the contribution of the prophages loci to the genetic diversity of CLas was investigated in several studies (Deng et al., ; Liu et al., , ; Puttamuk et al., , ; Tomimura et al., ; Villechanoux, Garnier, Laigret, Renaudin, & Bové, ; Wang, Zhou, Deng, Su, & Chen, ; Zhou et al., ).…”

Draft Genome Sequence of “ Candidatus Liberibacter asiaticus” from California

“…L. asiaticus”-infected citrus trees have been found in California. A recent study showed that the California strain was similar to strains in the Asiatic group ( 6 ).…”