Overall, the major clades are in large agreement with previous studies based on fewer genomes and single genes, such as 16S rRNA or parts thereof [ 18- 21].
These earlier analyses, however, were based on fewer genome sequences (4 – 5) and used a 'strict' definition of core genome, including only genes that were present in 100% of strains.
Molecular studies have been based on few individual genes, essentially 18S, 28S, 16S, and COI data [ 2- 5], or few complete mitochondrial genomes [ 6- 8].
Estimates based on few patients are simply more uncertain.
Because every bacterial isolate is potentially an unrepresentative mutant and due to the imperfect nature of NGS assemblies, the core genome cannot be simply defined as the genes present in all isolates; however, the estimate of a core genome comprising 1605 genes generated here is in good agreement with other estimates (1532-1706) wereh were based on substantially fewer genomes [ 23, 37, 58, 59].
With the exception of a few population studies based on complete genomes [36], [37] or coding region segments [38], [39], [40], most of the genotyping studies carried out to date were based on control region sequences [8] and/or mtSNPs at a low to moderate level of hg definition [18], [19], [20], [21], [41], [42].
While Xg and Xv show close relationship to Xcc based on whole genome comparisons, few pathogenicity clusters mentioned above seem to be conserved among tomato/pepper xanthomonads.
Previous results based on substantially fewer mitochondrial genome sequences are consistent with the current conclusions based on broader taxon sampling, for example, support for a sister-group relationship between Ascaridida and Rhabditida [ 20] and absence of monophyly for representative clade III species [ 21].
Phylogenetic analyses that are based on even complete genomes of relatively few taxa are likely to result in strongly supported, but incorrect, evolutionary reconstructions [ 16, 17, 47].
Celera will make public a reference DNA sequence based on the genomes of all these individuals.
