Phylogeographic Analysis of Soft-Rot-Causing Pectobacterium spp. Strains Obtained from Cabbage in Serbia

Abstract

The aim of this study was to establish a link between genetic diversity and the geographic origin of Pectobacterium strains belonging to three species-P. carotovorum, P. versatile, and P. odoriferum-isolated from cabbage in Serbia by comparing their sequences with those of strains sourced from different hosts and countries in Europe, Asia, and North America. Phylogeographic relatedness was reconstructed using the Templeton, Crandall, and Sing's (TCS) haplotype network based on concatenated sequences of the housekeeping genes dnaX, icdA, mdh, and proA, while pairwise genetic distances were computed by applying the p-distance model. The obtained TCS haplotype networks indicated the existence of high intra-species genetic diversity among strains of all three species, as reflected in the 0.2-2.3%, 0.2-2.5%, and 0.1-1.7% genetic distance ranges obtained for P. carotovorum, P. versatile, and P. odoriferum, respectively. Five new haplotypes (denoted as HPc1-HPc5) were detected among cabbage strains of P. carotovorum, while one new haplotype was identified for both P. versatile (HPv1) and P. odoriferum (HPo1). None of the TCS haplotype networks provided evidence of significant correlation between geographic origin and the determined haplotypes, i.e., the infection origin. However, as haplotype network results are affected by the availability of sequencing data in public databases for the used genes and the number of analyzed strains, these findings may also be influenced by small sample size.

Keywords: Pectobacterium; TCS haplotype network; cabbage; phylogeographic analysis.

Figure 1

(a) Templeton, Crandall, and Sing’s (TCS) haplotype network showing the phylogeographic position of the five tested Serbian P. carotovorum strains (Pc2321, Pc3821, Pc4821, Pc5421, and Pc8321) and seven reference P. carotovorum strains (ATCC 15713, 25.1, WPP14, BP201601.1, JR1.1, XP-13, and Pcc2520). Different colors on the TCS network represent countries in which the tested/reference strains were isolated. The number of hatch marks reflects the number of nucleotide differences detected between haplotypes, while the arrow points to an ancestral genotype; (b) World map showing the distribution of the 12 detected haplotypes (HPc1–HPc12) of the tested and reference P. carotovorum strains by country.

Figure 2

(a) Templeton, Crandall, and Sing’s (TCS) haplotype network showing phylogeographic position of one tested Serbian P. versatile (Pv6321) strain and nine reference P. versatile strains (14A, 3-2, SCC1, F131, DSM 30169, MYP201603, SR1, SR12, and Pv1520). Different colors on the TCS network represent countries in which the tested/reference strains were isolated. The number of hatch marks reflects the number of nucleotide differences detected between haplotypes; (b) World map showing the distribution of the 10 detected haplotypes (HPv1–HPc10) of the tested and reference P. versatile strains by country.

Figure 3

(a) Templeton, Crandall, and Sing’s (TCS) haplotype network showing the phylogeographic position of one tested Serbian P. odoriferum (Po7521) strain and three reference P. odoriferum strains (BC S7, JK2.1, and CFBP 1878). Different colors on the TCS network represent countries in which the tested/reference strains were isolated. The number of hatch marks denotes the number of nucleotide differences detected between haplotypes, while the arrow points to an ancestral genotype; (b) World map showing the distribution of the four detected haplotypes (HPo1–HPo4) of the tested and reference P. odoriferum strains by country.