Skip to main content
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 #311469

Research Project: Epidemiology and Management of Pierce's Disease and Other Maladies of Grape

Location: Crop Diseases, Pests and Genetics Research

Title: Analyses of Xylella whole genome sequences and proposal of Xylella taiwanensis sp. nov.

Author
item Chen, Jianchi
item Su, C - Taiwan Agricultural Chemicals And Toxic Substances Research Institute
item Deng, W - National Chung-Hsing University
item Jan, F - National Chung-Hsing University
item Chang, C - University Of Georgia
item Huang, H - University Of South Florida

Submitted to: CDFA Pierce's Disease Control Program Research Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 12/15/2014
Publication Date: 12/15/2014
Citation: Chen, J., Su, C.C., Deng, W.L., Jan, F.J., Chang, C.J., Huang, H. 2014. Analyses of Xylella whole genome sequences and proposal of Xylella taiwanensis sp. nov. CDFA Pierce's Disease Control Program Research Symposium. p.92.

Interpretive Summary:

Technical Abstract: Xylella fastidiosa is a Gram negative, xylem limited and nutritionally fastidious plant pathogenic bacterium that cause disease in many economically important plants. A single species, fastidiosa, with three subspecies (fastidiosa, multiplex, and pauca) have been described. Most Xylella strains were reported from North or South Americas. However, reports from other continents are emerging. For example, a Xylella strain was found in Taiwan causing pear leaf scorch (PLS) disease in the area where the low-chilling pear cultivar Hengshan (Pyrus pyrifolia) was grown. Current taxonomy of X. fastidiosa is anchored around whole genome DNA-DNA hybridization (DDH) relativeness. DDH is a gold standard for bacterial species delineation. Yet, DDH is labor intensive and its use for analyses of multiple X. fastidiosa strains is limited or even prohibitive. Thanks to the advancement of next generation sequencing (NGS), whole genome sequencing of X. fastidiosa strains is feasible and sequences are accumulating. Average Nucleotide Index (ANI) calculated from whole genome sequence comparisons has been introduced for the replacement of DDH in bacterial taxonomy. The current version of GenBank sequence database has 17 whole genome sequences of X. fastidiosa including a PLS strain, PLS229. In this study, ANI values were calculated from available whole genome sequences of Xylella strains and a phylogenic relative strain, Xanthomonas campestris pv. campestris. Substantiated by the analyses of 16S rRNA gene and 16S-23S intergenic transcribed spacer (ITS) sequences, ANI analyses have supported previous taxonomic establishment of grouping all American strains of X. fastidiosa into a single species (ANI>95). ANI analyses also have further identified thresholds to define the three previously established subspecies. Lastly, ANI has delineated a proposed new species, X. taiwanensis, for the PLS strain from Taiwan.