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Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species

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Abstract

A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30–33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies ‘sandyi’ and ‘morus’ are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results.

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Acknowledgments

The study was financed by the ordinary funds of the Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria.

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  1. Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria – Centro di ricerca per le Colture Arboree, Via di Fioranello, 52, 00134, Rome, Italy

    Simone Marcelletti & Marco Scortichini

  2. Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria – Centro di ricerca per le Colture Arboree, Via Torrino, 3, 81100, Caserta, Italy

    Marco Scortichini

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  1. Simone Marcelletti
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Correspondence to Marco Scortichini.

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Communicated by Erko Stackebrandt.

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Table S1

Whole-genome-based average nucleotide identity (ANI) values regarding 20 Xylella fastidiosa strains, the diverging PLS 229 and the outgroup Xanthomonas oryzae pv. oryzae KACC 10331. The strains of subspecies pauca showed ANI values ranging from 95 to 96 % (XLS 25 kb)

Table S2

Tetranucleotide frequency correlation coefficients (TETRA) values of 20 Xylella fastidiosa strains, the diverging PLS 229 and the outgroup Xanthomonas oryzae pv. oryzae KACC 10331 (DOC 86 kb)

Supplementary Figure S1

Phylogenetic relationships among 21 strains of Xylella fastidiosa as obtained with multilocus sequence typing (MLST) analysis using 6.021 concatenated nucleotides of seven housekeeping genes (gltT, holC, lacF, leuA, nuoL, petC, rfbD) with bootstrap values shown at the nodes. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 was included as outgroup (TIFF 3938 kb)

Supplementary Figure S2

Recombination network among 20 Xylella fastidiosa strains built using gltT gene. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 included as outgroup and the strain PLS 229 resulted divergent from the genuine X. fastidiosa strains and are not shown. (PDF 16 kb)

Supplementary Figure S3

Recombination network among 20 Xylella fastidiosa strains built using holC gene. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 included as outgroup and the strain PLS 229 resulted divergent from the genuine X. fastidiosa strains and are not shown (PDF 23 kb)

Supplementary Figure S4

Recombination network among 20 Xylella fastidiosa strains built using lacF gene. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 included as outgroup and the strain PLS 229 resulted divergent from the genuine X. fastidiosa strains and are not shown (PDF 22 kb)

Supplementary Figure S5

Recombination network among 20 Xylella fastidiosa strains built using leuA gene. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 included as outgroup and the strain PLS 229 resulted divergent from the genuine X. fastidiosa strains and are not shown (PDF 20 kb)

Supplementary Figure S6

Recombination network among 20 Xylella fastidiosa strains built using nuoL gene. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 included as outgroup and the strain PLS 229 resulted divergent from the genuine X. fastidiosa strains and are not shown. (PDF 42 kb)

Supplementary Figure S7

Recombination network among 20 Xylella fastidiosa strains built using petC gene. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 included as outgroup and the strain PLS 229 resulted divergent from the genuine X. fastidiosa strains and are not shown (PDF 16 kb)

Supplementary Figure S8

Recombination network among 20 Xylella fastidiosa strains built using rfbD gene. The scale bar indicates the number of substitution per nucleotide position. Strain legend is shown in Table 1. Xanthomonas oryzae pv. oryzae KACC 10331 included as outgroup and the strain PLS 229 resulted divergent from the genuine X. fastidiosa strains and are not shown (PDF 16 kb)

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Marcelletti, S., Scortichini, M. Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species. Arch Microbiol 198, 803–812 (2016). https://doi.org/10.1007/s00203-016-1245-1

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