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Southern shagbark hickory (Carya carolinae-septentrionalis) is one of several deciduous trees in the family Juglandaceae and genus Carya that are native to North America. Southern shagbark hickory has a restricted distribution to the Southeast U.S.A. (USDA, 2024). During a disease survey in September, 2023, symptoms of leaf scorch were noticed on trees planted in a hickory collection at the USDA-ARS, Byron, GA. Scorch was characterized by tan to light brown, irregularly shaped necrotic lesions often starting along the leaf margins, with the necrosis spreading across the entire leaflet, resulting in curling of leaflet and in some cases affecting the whole leaf (Supplementary Fig. 1). Some defoliation of leaflets on compound leaves was noted. Symptomatic shoot terminals with compound leaves were collected, stored in a refrigerator (~4°C) and processed within three days. The epidermis was stripped from a sample of leaflet petioles and ground with a tissuelyser. DNA was extracted from the petiole sample using a Zymo Research® kit (Quick-DNA™ Fungal/Bacterial Kit, Zymo Research®, Irvine, CA) following the manufacturer's protocol. Conventional PCR was performed on the sample with positive controls (DNA of Xylella strain M12) and negative controls (water, healthy pecan) using four previously characterized Xylella fastidiosa (Xf)-specific primer sets (Francis et al., 2006; Minsavage et al. 1994; Rodrigues et al., 2003). The resulting amplicons each had the characteristic size expected for X. fastidiosa. A further two samples of DNA were extracted using a NucleoSpin Plant II kit (Machereey-Nagel, Duren, Germany) following the manufacturer's protocol. The DNA samples were tested by SYBR-green real-time PCR with primer sets Teme150fc/Teme454rg (specific to Xf subsp. fastidiosa, Xff) and Dixon454fa/Dixon1261rg (specific to Xf subsp. multiplex, Xfm) (Chen et al., 2005), yielding Ct values of 31.39 and 18.96, respectively, suggesting dominant Xfm infection. One sample (designated Cc-sR5T1) was further selected and subject to next generation sequencing (NGS) using an Illumina NovaSeq 6000 (PE150) platform. A total of 58,601,960 paired reads were generated with a mapping rate of 0.97% to Xfm M12 (NC_010513.1) and 0.95% to Xff M23 (NC010577.1) using Bowtie2 (Langmead and Salzberg, 2012), confirming the Xfm status of strain Cc-sR5T1. Read coverages on both M12 and M23 genomes were >60X. Top-5 and bottom-5 reads in the mapped read data sets were selected and used as queries for a BLAST search against the National Center for Biotechnology Information (NCBI) core-nr database. All top hits were Xf subsp. multiplex (query coverage = 97 to 100%, Percentage Identity = 99 to 100%) with one exception likely related to the region of a mobile element (Supplementary Table 1). In summary, a Xfm strain was identified in a shagbark hickory tree based on leaf scorch symptoms, PCR characteristic loci, and NGS whole genome approaches. The pathogen Xfm infects other Carya (Hilton et al. 2020), including C. illinoinensis (pecan) (Sanderlin and Heyderich-Alger, 2000), which is an economically important nut crop in the southern U.S.A. Shagbark hickory is not of high economic value, but now a possible reservoir of Xfm. Knowledge of the causal agents of the disease in Carya species is important for disease management purposes in both agricultural plantings and natural stands of trees. Furthermore, Xylella pathogens have both national and international phytosanitary ramifications.

" Candidatus Liberibacter asiaticus" (CLas) is associated with citrus huanglongbing, a severe disease with global importance that affects citrus production in Brazil. This study reports the first complete genome of a Brazilian strain of CLas. The genomic structure comparison of strain 9PA with those of 13 complete CLas genomes revealed 9,091 mismatches and 992 gaps/insertions, highlighting eight locally colinear blocks, among which six are in the prophage region. Phylogenetic analysis categorized 13 CLas genomes into two clusters with 9PA clustered with strains from China and the United States. Whole-genomic comparison identified diverse hypervariable genomic regions (HGRs). Three HGRs in the chromosomal region and three in the prophage region were selected and investigated by polymerase chain reaction. HGRs assessed from 68 samples, from medium- to high-huanglongbing incidence areas in Sao Paulo state, were grouped into haplotypes A to P. Haplotype A, which includes strain 9PA, is the second most prevalent, representing 19.1% of the samples. Haplotype B, the most common, accounts for 42.6%. Together with haplotype C, these make up 72% of the evaluated samples. The 9PA strain has prophage P-9PA-1, both integrated and circularized, and P-9PA-3, only found in a circularized form. Prophages show high identity with SC1 (83%) and P-JXGC-3 (98%). Co-occurrence of both type 1 and 3 prophages was observed in field samples. The approach employed provides insights into the Brazilian CLas population, providing markers for population studies and highlighting the prevalence of type 1 and 3 prophages in the population., Importance: CLas is a destructive pathogen responsible for causing the severe citrus disease known as huanglongbing. Our study presents the first fully sequenced Brazilian strain of CLas, designated as 9PA, and includes an analysis of two prophages occurring in this strain. The main objective of our research was to compare the genome features of this Brazilian strain with other fully sequenced genomes and to identify its hypervariable genetic regions. These regions were subsequently used to assess genomic variability within both the chromosomal and prophage regions in Brazilian isolates of CLas. Our findings offer valuable insights into the diversified adaptation of CLas., Competing Interests: The authors declare no conflict of interest.