- Costa Rica) two X.. - Using whole genome sequences, the patterns of gene gain/loss, genomic introgression, and genetic diversity were characterized within Costa Rica and contrasted to other X. - fastidiosa in Costa Rica were consistent with those of other native populations (i.e. - fastidiosa subspe- cies present in Costa Rica is of value in increasing our knowledge on X. - pauca within Costa Rica. - In order to address both points we contextualize our findings within Costa Rica by comparing them to other X. - Overall, three main comparisons are ex- plored: 1) between populations of the same subspecies (e.g., California, Southeastern US, Spain, Taiwan, and Costa Rica for subsp. - and Italy, Brazil, and Costa Rica for subsp. - Costa Rica subsp. - fastidiosa, and the role that Costa Rica has in it.. - Except for Costa Rica (n = 13) and Brazil (n = 3), all data included in this study have been previously made publicly available. - The use of genetic resources from Costa Rica was approved by the Institutional Biodiversity Committee of the University of Costa Rica (VI according to the Biodiversity Law #7788 and the Convention on Biological Diversity.. - fastidiosa Costa Rica XF68 Psidium spp. - relative to XF70 on the ML trees generated from the Costa Rica dataset (see later methods). - Within the Costa Rica dataset, Roary ’ s presence/ab- sence matrix was used to calculate variations on the core genome size on each node of the ML tree. - These numbers were visualized using a cladogram of the Costa Rica isolates. - Detection of recombinant sequences within the Costa Rica data set. - FastGEAR [48] was used with default parameters to identify lineage-specific recombinant segments (ances- tral) and strain-specific recombinant segments (recent) in the core genome alignment of the Costa Rican data- set. - pauca isolates from Brazil were also calculated and compared to those observed within the Costa Rica population.. - To evaluate the relation of this lineage with other Costa Rica isolates, each recombinant segment involving the. - of the larger dataset, which included subsp. - fastidiosa from Costa Rica and the published COF0407 genome (XFAS006-SEQ-1-ASM-1) as a model for subsp. - pauca from Costa Rica. - pauca isolates from Costa Rica (n = 3).. - The Rozas’ ZZ index was used to identify LD values across the length of the core genome align- ment using a bin size of 500 nucleotides. - vinifera in Costa Rica [61]. - fas- tidiosa strains is likely to occur in Costa Rica.. - A total of 4816 genes were identified in the Costa Rica dataset (12 strains for subsp. - Likewise, the number of strain-specific genes was similar regardless of the host- plant species.. - While most gene gain/loss events occur at the subspecies split, genetic gain/loss is actively occurring within each subspecies in Costa Rica. - Complex recombination patterns are observed within Costa Rica X. - The core genome alignment for the Costa Rica dataset was used to evaluate the frequency, size, and location of recom- bination events. - Overall, in relation to other strains in Costa Rica ‘unknown’ sequences were either ancestral to other subsp. - fastidiosa lineages circulating within Costa Rica. - Furthermore, 71 of these 73 events were also found in the core genome of the complete dataset (N = 261) (Supplementary figure 5). - pauca isolates originating from Costa Rica.. - fastidiosa ( N This study, Costa Rica (N . - Finally, a comparison of the number and nature of the recombination events within Brazil and Costa Rica (na- tive regions to subsp. - fastidiosa isolates from Costa Rica (Fig. - fastidiosa, both π and H showed higher levels of diversity in Costa Rica compared to California (Table 3). - pauca (yellow) from Costa Rica plants. - pauca, both genetic and haplotype di- versity were higher in Brazil isolates compared to both Costa Rica and Italy (Table 3). - pauca from Costa Rica was likely affected by the low sample size (n = 3). - genomes at present, laboratory assays confirm its pres- ence in Costa Rica and its virulence to local flora [63, 64].. - fasti- diosa populations in California, Southeastern US, and Costa Rica had negative Tajima’s D estimates, with the. - fastidiosa subspecies in Costa Rica. - FastGEAR recombination plot showing donor/recipient sequences and the position of the recombinant event in the alignment. - magnitude of these values being larger in California compared to Southeastern US and Costa Rica. - Furthermore, Wat- terson’s θ estimates were comparable between the Costa Rica and Southeastern US populations, but higher in California, Spain, and Taiwan. - Both Tajima’s D and LD (measured using the Rozas’ ZZ) estimates varied across the length of the core genome alignment (Supplementary figure 6 and 7). - pauca in Costa Rica. - population were highly variable across the length of the core genome, thought they largely remained positive. - fastidiosa, Tajima’s D estimates also varied across the length of the genome, particularly in the Costa Rican population. - fastidiosa in Costa Rica), the. - 3 Brazil and Costa Rica lineage- and strain-specific recombination circular plots. - Orange box includes isolates representing the two monophyletic clades/subspecies found within Costa Rica: X. - Costa Rica: Psidium spp. - Table3Geneticdiversity(π),haplotypediversity(H),Watterson(θ),andTajima’sDofX.fastidiosasubsp.fastidiosa(CaliforniaUSandCostaRica)andX.fastidiosasubsp.pauca (Italy,CostaRica,andBrazil)withandwithoutrecombinantregions PopulationWithrecombinationWithoutrecombination SNPsCore(nt)Nucleotide diversity(π)Haplotypediversity(H)Watterson’sestimator(θ)Tajima’sDSNPsCore(nt)Nucleotidediversity(π)Haplotypediversity(H)Watterson’sestimator(θ)Tajima’sD X.fastidiosasubsp.fastidiosa California x10e−056.87x10e−075.85x10e x10e−059.87x10e−076.35x10e−05−0.912 CostaRica x10e−037.14x10e−073.44x10e x10e−031.04x10e−063.47x10e−03−0.385 SouthEastUS(9)12062.97x10e−047.14x10e−073.17x10e x10e−041.04x10e−063.62x10e−04−0.441 Spain(3)31.43x10e−067.14x10e−071.42x10e−06*21.39x10e−061.04x10e−063.39x10e−06* Taiwan(2)64.28x10e−067.14x10e−074.28x10e−06*44.18x10e−061.04x10e−064.18x10e−06* X.fastidiosasubsp.pauca Italy x10e−065.01x10e−076.45x10e x10e−064.09x10e−077.07x10e−06−2.234 Brazil x10e−031.90x10e−062.58x10e x10e−033.53x10e−062.54x10e−030.731 CostaRica(3)33.92x10e−061.96x10e−063.92x10e−06*25.09x10e−063.82x10e−065.09x10e−06* *CostaRicasubsp.paucaisolates(N=3)werenotincluded *Spainsubsp.fastidiosaisolates(N=3)werenotincluded *Taiwansubsp.fastidiosaisolates(N=2)werenotincluded. - Rozas’ ZZ index varied largely across the length of the core genome. - fastidiosa strains from Costa Rica do not cause disease in V. - fas- tidiosa from Costa Rica is not capable of successfully in- fecting V. - The core genome shared by both subspecies within Costa Rica was roughly 86% of the size of the core gen- ome of subsp. - fastidiosa’s core genome and 67% of the size of subsp. - (2019) incorporated isolates from popula- tions of diverse geographical origins, while Costa Rica rep- resents a single geographic point. - all isolates ori- ginate from plant species introduced to Costa Rica: Cof- fea spp. - colonization of the same host species and pathogen specialization.. - These isolates formed a monophyletic group within the Costa Rica dataset and a gradient leading to the introduction to the continental US when the entire subsp. - fastidiosa isolates within Costa Rica. - Previous studies have suggested that homologous recombination leads to homogenization of the core genome in bacteria [71]. - The direction of donor/recipient strains within Costa Rica changed with evolutionary time. - The low genetic di- versity of the subsp. - At a whole genome level, the nucleo- tide diversity in Costa Rica was the highest of all evalu- ated populations (Costa Rica, 14,573 SNPs and π = 3.18x10e − 03 . - Without recombining regions, the Costa Rica population has a higher mutational rate estimate than Southeastern US. - Moreover, there is a strong association between appearance of symptoms in oleander plants from Costa Rica and the detection of clade ST53. - Thus, host-specific adaptations could also contribute to the higher genetic diversity of the region.. - On the other hand, both California and the Southeastern US populations showed a few positive peaks scattered across the length of the core genome alignment. - fastidiosa strains from Costa Rica were not capable to cause disease symptoms in V. - fastidiosa from Costa Rica is ancestral to other geographic locations. - Costa Rican isolates are found at the base of the subsp. - fastidiosa subspecies found within Costa Rica are highly malleable. - Costa Rica) influences the evolutionary outcome of a world-wide pathogen such as X. - fastidiosa and pauca isolates originating from Costa Rica.. - fastidiosa isolates in Costa Rica.. - FastGEAR recombination plot showing donor/recipient recombinant sequences and the position of the recombinant event in the alignment. - Placement of ‘ unknown ’ lineages identified in recent recombination events within Costa Rica. - fastidiosa isolate from Costa Rica and an ‘ unknown ’ lineage located within the complete dataset. - Nucleotide diversity (Tajima ’ s D) and recombinant events across the length of the core genome alignment. - fastidiosa in Costa Rica (orange), subsp. - fastidiosa : Line plot showing Tajima ’ s D values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among identified clusters. - pauca : Line plot showing Tajima ’ s D values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among identified clusters. - Linkage Disequilibrium (Rozas ’ ZZ) and recombinant events across the length of the core genome alignment. - fastidiosa : Line plot showing Rozas ’ ZZ values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among identified clusters. - pauca : Line plot showing Rozas ’ ZZ values across the length of the core genome alignment and fastGEAR output showing the location of recombination events among identified clusters. - fastidiosa in Costa Rica (orange, above) and X. - Update of the Xylella spp. - Isolation and molecular characterization of Xylella fastidiosa from coffee plants in Costa Rica. - Confirmation of Xylella fastidiosa infecting grapes Vitis vinifera in Costa Rica. - First Report of Xylella fastidiosa in Nerium oleander in Costa Rica. - El café en Costa Rica. - Xylella fastidiosa
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