Whole genome resource for Xylella fastidiosa subsp. multiplex strain GaT2 causing pecan bacterial leaf scorch in Georgia, United States

Authors: Hilton, Angelyn; Bock, Clive; BRENNEMAN, TIM - University Of Georgia; Chatwin, Warren; Chen, Jianchi

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2025
Publication Date: 5/5/2025
Citation: Hilton, A.E., Bock, C.H., Brenneman, T., Chatwin, W.B., Chen, J. 2025. Whole genome resource for Xylella fastidiosa subsp. multiplex strain GaT2 causing pecan bacterial leaf scorch in Georgia, United States. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-09-24-0103-A.
DOI: https://doi.org/10.1094/PHYTOFR-09-24-0103-A

Interpretive Summary: Xylella fastidiosa is a bacterial pathogen that causes Pecan Bacterial Leaf Scorch disease in pecan. The disease is widespread across the entire pecan growing region of the United States, and can lead to significant yield losses in highly susceptible cultivars. The pathogen is slow-growing and challenging to isolate into pure culture. Therefore, little molecular research has been performed and no genomic DNA sequence is currently available. In this study, DNA samples were isolated from a symptomatic cv. Byrd pecan tree in Albany, Georgia. Next generation sequencing was performed to obtain a metagenomic sequence. Bioinformatic analysis using a reference guided assembly approach was used to derive the pecan Xylella fastidiosa genome sequence from the original total metagenomic sequence. When compared to a database of other bacterial genomes, the newly assembled, draft Xylella genome was determined to be 100% complete with 147 contigs and a length of 2.5 megabases. This new genome will serve as a valuable resource for the continued study of Xylella fastidisoa in pecan, with the goal of eliminating Xylella as a significant impediment to efficient pecan production in the United States.

Technical Abstract: Xylella fastidiosa is a xylem-limited, endophytic bacterium that can infect over 600 plant species, including hardwood trees such as olive, oak, peach, sycamore, and pecan. Pecan bacterial leaf scorch (PBLS) is caused by X. fastidiosa and the disease is endemic in areas where pecan (Carya illinoinensis) is cultivated in the U.S.A. In vitro culturing of X. fastidiosa is challenging due to its fastidious growth habits that require nutritionally complex culture media. Therefore, biological data on many strains of X. fastidiosa are limited. No genomic sequence of X. fastidiosa PBLS strain has been obtained. In this study, we report the whole genome sequence of X. fastidiosa subsp. multiplex isolate GaT2 from a symptomatic PBLS pecan tree (cv. Byrd) in Albany, Georgia. Metagenomic DNA was extracted and the presence of Xylella fastidiosa was confirmed by qPCR. Genome sequencing was performed using an Illumina NovaSeq 6000 PE150, and GaT2 DNA sample yielded a total of 40,546,031,100 bp in 270,306,874 reads (read size = 150 bp) with a mean Q score = 36.85 (97.44% > Q30). The sequence reads were aligned against the pecan chloroplast reference genome and filtered prior to aligning the remaining sequence reads against 12 different representative, chromosomal genomes of Xylella fastidiosa using Bowtie2 with default parameters. SPAdes was then used to de novo assemble the alignment with the lowest number of contigs, the largest mapped contigs, and highest percent of mapped reads. Prokka was used to annotate the genome, and BUSCO was run in genome mode to determine the completeness based on the prodigal gene predictor and the Bacteria lineage dataset consisting of 124 BUSCOs. The GaT2 genome was determined to be 100% complete with 147 contigs and a length of 2.5 megabases. This new genome will serve as a valuable resource for the continued study of Xylella fastidisoa in pecan.