Phylogenomic analysis of 343 Xanthomonas citri pv. citri strains unravels introduction history and dispersal paths.

"plos publication stage vor-update-to-uncorrected-proof publication update 2023-12-29 data availability the raw sequencing reads of genomic data and assembled genomes were deposited in the ncbi database under the accession number prjna833305.; data availability the raw sequencing reads of genomic data and assembled genomes were deposited in the ncbi database under the accession number prjna833305. the genomic sequences and analysis scripts were deposited at zenodo ( https://zenodo org/records/10015036 ).; the genomic sequences and analysis scripts were deposited at zenodo ( https://zenodo org/records/10015036 ). the ncbi accession ids of biosample raw data and assembled genomes were showed in tab b in s1 dataset .; the ncbi accession ids of biosample raw data and assembled genomes were showed in tab b in s1 dataset .; in total we sequenced the genomes of 343 xcc strains collected over 20 years (from 1997 to 2016) from various citrus groves in 20 florida counties ( fig 1 and tab a in s1 dataset ).; the average of genome completeness for each strain was98 3% (range: 97 43% to 98 44%) and 100% (range: 99 64% to 100%) as estimated by comparing with reference genome of xcc 306 and single copy marker genes respectively (tab b in s1 dataset ).; on average 4445 genes were predicted for each genome (tab b in s1 dataset ).; the average nucleotide identity (ani) values among the 343 newly sequenced strains and xcc 306 were 99 96-99 99% (tab c in s1 dataset ).; the ani values among 343 newly sequenced strains and pathotypes xcc a w or xcc a* ranged from 99 54% to 99 56% and 99 61% to 99 64% respectively (tab c in s1 dataset ).; these results suggest that the 343 xcc strains belong to pathotype a these strains exhibited a high degree of conservation in genomic sequence despite being isolated from different citrus cultivars at different times and in different locations ( fig 2 and tab a in s1 dataset ) 10 1371/journal ppat 1011876 g001 fig 1 a geographic distribution of sampling sites b host distribution of 343 samples c time distribution of 343 samples.; among these accessory genes216 were present in only one strain and 177 were unique to the reference strain xcc 306 (tab d in s1 dataset ).; in addition to the newly sequenced 343 strains10 publicly available genomes of xcc from florida were also included for analyses (tab a in s1 dataset ).; cluster 1 and cluster 2 comprised 21 and 332 strains respectively (tab a s1 dataset ).; furthermore we collected 431 publicly available genomes of xcc a strains from around the world (tab e in s1 dataset ).; additionally genes associated with pathogenicity and fitness including those involved in chemotaxis t3ss and effectors t2ss t4ss t6ss t4 pilus flagella rpf regulator iron metabolism polysaccharide utilization enzymes biofilm formation and kinases contained non-synonymous snps or indels (tab f in s1 dataset ).; shotgun genomic library preparation and sequencing of 343 samples (tab a in s1 dataset ) were performed per the manufacturer's protocol using the bgiseq500 platform at bgi-shenzhen china as previously described [ ].; on average more than 1435 million bp (mb) of raw data were generated for each strain (tab b in s1 dataset ).; the summary of genome sequencing assembly and gene prediction for the 343 xcc a strains is provided in tab b in s1 dataset .; we performed a comparative genomic analysis of 351 xcc strains (tab a in s1 dataset ) including the 343 newly sequenced strains from bgiseq in this study 7 strains from a previous study [ ] and the reference strain xcc 306.; the snps and indels across the genomes of the 343 newly sequenced florida xcc strains and 439 publicly available xcc strains (tabs a and e in s1 dataset ) were identified by mapping the raw short reads to the reference genome of xcc 306 using bowtie2 version 2 2 6 [ ] and samtools version 1 2 [ ].; green and purple indicate cluster 1 and cluster 2 respectively (tif) click here for additional data file s2 fig venn plot depicting the number of genes (a) and genomic mutations (b) among the two clusters of xcc a strain (tif) click here for additional data file s1 dataset b the summary of genome sequencing assembly gene prediction and ncbi accession information of 343 xcca strains. s1 table (xlsx data availability the raw sequencing reads of genomic data and assembled genomes were deposited in the ncbi database under the accession number prjna833305"

"the genomic sequences and analysis scripts were deposited at zenodo ( https://zenodo org/records/10015036 ).; the genomic sequences and analysis scripts were deposited at zenodo ( https://zenodo org/records/10015036 )."

"The authors declare no competing interests."

"This project was supported by funding from Florida Citrus Initiative Program, U.S. Department of Agriculture National Institute of Food and Agriculture grant 2021-67013-34588, 2016-70016-24833, FDACS Specialty Crop Block Grant Program AM22SCBPFL1125, and Hatch project [FLA-CRC-005979] to NW. The funder was not involved in the study design, data collection and analysis, decision to publish, or preparation of the manuscript."