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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 #327300

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

Location: Crop Diseases, Pests and Genetics Research

Title: Evaluation of assembling methods on determination of whole genome sequence of Xylella fastidiosa blueberry bacterial leaf scorch strain

Author
item Chen, Jianchi
item Wallis, Christopher
item Chang, C.j. - University Of Georgia

Submitted to: American Phytopathological Society Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 5/16/2016
Publication Date: 7/30/2016
Citation: Chen, J., Wallis, C.M., Chang, C. 2016. Evaluation of assembling methods on determination of whole genome sequence of Xylella fastidiosa blueberry bacterial leaf scorch strain. American Phytopathological Society Abstracts. 106:S4.27.

Interpretive Summary:

Technical Abstract: Blueberry bacterial leaf scorch (BBLS) disease, a threat to blueberry production in the Southern USA and potentially elsewhere, is caused by Xylella fastidiosa. Efficient control of BBLS requires knowledge of the pathogen. However, this is challenging because Xylella fastidiosa is difficult to culture. The objective of this study was to initiate characterization of a BBLS strain based on whole genome sequence. A total of 13,739,924 sequence paired reads (mean = 251 bp) were generated from a BBLS strain isolated from Georgia, USA. Draft whole genome sequences (minimum contig size = 1,000 bp) were generated by both de novo assembling (DA) and referenced assembling (RA) using CLC Genomic Workbench version 7.5. The DA draft genome was 2,537K (95 contigs). Sizes of RAs varied depending on referenced genome sequences used: 2,449K (39 contigs) with NC_010513 (M12, subsp. multiplex), 2,461K (70 contigs) with NC_010577 (M23, subsp. fastidiosa), 2,467K (96 contigs) with NC_004556 (Temecula1, subsp. fastidiosa), and 2,457K (180 contigs) with NC_002488 (9a5c, subsp. pauca). Percentage coverages were 99.0% (M12), 97.1% (M23), 97.1% (Temecula1) and 91.7% (9a5c). Average Nucleotide Identity (ANI) values were 99.9 (M12), 97.5 (M23), 97.6 (Temecula1) and 96.2 (9a5c). All these data suggest that 1) DA alone was promising yet contig number remained high; 2) For RA, reference genome sequence had significant influence on the BBLS genome size; and 3) BBLS strain is a member of Xylella fastidiosa subsp. multiplex based on similarity to strain M12.