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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 #382961

Research Project: Identification of Novel Management Strategies for Key Pests and Pathogens of Grapevine with Emphasis on the Xylella Fastidiosa Pathosystem

Location: Crop Diseases, Pests and Genetics Research

Title: Genome rearrangements of Xylella fastidiosa strains in US and updates on X. taiwanensis

item Chen, Jianchi
item SU, C.C - Agricultural Research Institute Of Taiwan
item SHIH, H.T. - Agricultural Research Institute Of Taiwan
item JAN, F.J. - Chung Hsing University
item CHANG, C.J. - University Of Georgia

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/29/2021
Publication Date: 4/29/2021
Citation: Chen, J., Su, C., Shih, H., Jan, F., Chang, C. 2021. Genome rearrangements of Xylella fastidiosa strains in US and updates on X. taiwanensis. Meeting Abstract. p.43.

Interpretive Summary:

Technical Abstract: Xylella fastidiosa is a Gram-negative and nutritionally fastidious bacterial pathogen causing Pierce’s disease (PD) of grapevine and other plant diseases in the USA. Xylella taiwanensis causes pear leaf scorch disease in Taiwan. Bacterial genomics is fundamental for the biological research and pathogen management. Current research in genomic variations of X. fastidiosa mostly focuses on single nucleotide polymorphisms (SNPs), short sequence insertions/deletions (Indels), and copy number variations (CNVs). Structural variations (SVs), e.g. chromosomal rearrangements, was reported between X. fastidiosa CVC strain (subsp. pauca) and PD strain (subsp. fastidiosa). In this study, the whole genome sequence of X. f. subsp. fastidosa strain ATCC 35879 causing PD in Florida was determined using PacBio RSII format. The ATCC 35879 genome has a circular chromosome of 2,565,504 bp with 2,904 predicted protein coding genes and 55 RNA genes, and a circular plasmid of 41,753 bp. The chromosomal sequence of strain ATCC 35879 was compared to that of X. f. subsp. fastidosa strain M23 causing both PD and almond leaf scorch disease in California. Genome rearrangements involving a ca. 1,200 Kbp region were detected. Genome annotations showed clusters of phage-related genes around the rearrangement junctions, suggesting the likely involvement of phage activities. Genome rearrangement events were also detected/confirmed between different subspecies of X. fastidosa and between X. fastidosa and X. taiwanensis. X. taiwanensis is the second species descripted under the genus Xylella in 2016. Little information about X. taiwanensis is available. DNA of a pear tree infected with X. taiwanensis was extracted and subjected to next generation sequencing (Illumina HiSeq). Metagenomic analysis on the sequence data detected a small plasmid of 2,193 bp. This plasmid showed > 65% similarities to plasmids from X. fastidiosa, Xanthomonas axonopodis and Stenotrohomonas maltophilia. Further genomic and metagenomic studies are underway.