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ARS Home » Southeast Area » Fort Pierce, Florida » U.S. Horticultural Research Laboratory » Subtropical Plant Pathology Research » Research » Publications at this Location » Publication #321123
Title: Comparative Genomics of multiple Candidatus Liberibacter asiaticus isolates reveals genetic diversity in Florida and provides clues to the evolution of the bacteria in citrus

Author
item WU, BO - Clemson University
item Duan, Ping
item Stover, Eddie
item MOORE, GLORIA - Clemson University
item Hartung, John
item JARA-CAVIERES, ANTONELLA - University Of Florida
item Shatters, Robert - Bob

Submitted to: International Research Conference on Huanglongbing
Publication Type: Abstract Only
Publication Acceptance Date: 10/15/2015
Publication Date: 3/30/2015
Citation: Wu, B., Duan, Y., Stover, E.W., Moore, G., Hartung, J.S., Jara-Cavieres, A., Shatters, R.G. 2015. Comparative Genomics of multiple Candidatus Liberibacter asiaticus isolates reveals genetic diversity in Florida and provides clues to the evolution of the bacteria in citrus [abstract]. J Cit Pathol. 2(1):45. iocv_journalcitruspathology_30222.

Interpretive Summary:

Technical Abstract: Understanding genetic diversity of within and among the populations of an organism provides information about the potential diversity in pathogenicity and susceptibility to host defenses as well as sustainable effectiveness of control treatments. A near whole genome sequencing strategy was used to conduct a genome diversity study of U.S. Candidatus Liberibacter asiaticus (CLas). Two thousand PCR primer pairs were designed using the PSY62 genome. Overlapping CLas genome fragments were amplified from total DNA of infected citrus from 35 locations (28 from Florida, 1 from California, 2 from Texas, and 4 international samples). All amplicons from each isolate were pooled as a “pseudogenome” and analyzed by NGS (Ion Torrent). Sequences were aligned to the Psy62 reference sequence and compared. On average, the isolate pseudogenomes covered 86.8% of the reference genome at an average of 740X coverage of each nucleotide. A total of 14,342 variations were identified, including 13,319 single nucleotide variations (SNVs) and 746 indels. Most of the prophage regions failed to amplify in only three isolates (California, Japan and Florida isolate FLCG-12). Three phylogenetically distinct genetic clusters of isolates were observed in Florida, with the Texas and California isolates being distinct but included in one of the three clusters. Seven isolates from adjoining trees in a single Florida grove, all clustered with PSY62, but displayed a total of 2189 variations, with non-reference alleles specific to each isolate and/or specific to this geographic group, suggesting rapid accumulation of variations. This analysis supports recombination and horizontal gene transfer between haplotypes within and among clusters. Among the variations there was an excess of harmful mutations expected to be deleterious such as open reading frame shifts, stop codon gains or start codon losses. Based on results, we hypothesize that genetic drift plays an important role in the evolution of this bacteria and could explain the fast accumulation of genetic variations.