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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #335388
Title: Whole genome sequence analyses revealed that strains of “Candidatus Liberibacter asiaticus” recently found in two California locations were different

Author
item ZHENG, Z - South China Agricultural University
item WU, F - South China Agricultural University
item KUMAGAI, L.B. - California Department Of Food And Agriculture
item Chen, Jianchi
item Polek, Marylou
item DENG, X - South China Agricultural University

Submitted to: International Research Conference on Huanglongbing
Publication Type: Abstract Only
Publication Acceptance Date: 2/1/2017
Publication Date: 3/14/2017
Citation: Zheng, Z., Wu, F., Kumagai, L., Chen, J., Polek, M., Deng, X. 2017. Whole genome sequence analyses revealed that strains of “Candidatus Liberibacter asiaticus” recently found in two California locations were different. International Research Conference on Huanglongbing.

Interpretive Summary:

Technical Abstract: ‘Candidatus Liberibacter asiaticus’ (CLas), an a-proteobacterium, is associated with citrus Huanglongbing (HLB; yellow shoot disease). In California, CLas was first detected in residential neighborhoods of Hacienda Heights (HH) in 2012 and San Gabriel (SG) in 2015. Although all infected trees were destroyed in compliance with a state mandate, citrus industry stakeholder concerns about HLB in California remain high. Little is known about the biology of CLas, particularly the California strains, hindering effective HLB management efforts. In this study, next generation sequencing (NGS) technology (Illumina MiSeq) was employed to characterize the HH and SG strains of CLas. Data sets containing >4 billion (Giga) bp of sequence were generated from each sample. Two prophages (P-HHCA1-2 and P-SGCA5-1) were identified by the consensus of mapping MiSeq reads onto two known Florida CLas prophage sequences, SC1 and SC2. P-HHCA1-2 was a SC2-like (100% coverage and 97% identity), or Type 2, prophage 38,920 bp in size. P-SGCA5-1 was a SC1-like (94% coverage and 96% identity), or Type 1, prophage 37,487 bp in size, spanning two contigs. Phylogenetic analysis revealed that P-HHCA1-2 was part of an Asiatic lineage within the Type 2 prophage group. Similarly, P-SGCA5-1 was part of an Asiatic lineage within Type 1 prophage group. The Asiatic relatedness of both P-HHCA1-2 and P-SGCA5-1 was further supported by the analysis of single nucleotide polymorphisms (SNPs) in the prophage terminase gene that has been established for CLas strain differentiation. The presence of different prophages suggests that the two California CLas strains could have been introduced from different sources. An alternative explanation is that there is a mixed CLas population containing the two types of prophages, and limited sampling in alternate geographic regions may not accurately depict true CLas diversity. More accurate pathway analysis may be achieved by genomic analysis of multiple isolates per geographic region.