Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in Serbia
The aim of this study was to establish a link between genetic diversity and the geographic origin of <i>Pectobacterium</i> strains belonging to three species—<i>P. carotovorum</i>, <i>P. versatile</i>, and <i>P. odoriferum</i>—isolated from cabbage in...
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MDPI AG
2023-08-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/8/2122 |
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| author | Aleksandra Jelušić Marco Scortichini Sanja Marković Petar Mitrović Renata Iličić Slaviša Stanković Tatjana Popović Milovanović |
| author_facet | Aleksandra Jelušić Marco Scortichini Sanja Marković Petar Mitrović Renata Iličić Slaviša Stanković Tatjana Popović Milovanović |
| author_sort | Aleksandra Jelušić |
| collection | DOAJ |
| description | The aim of this study was to establish a link between genetic diversity and the geographic origin of <i>Pectobacterium</i> strains belonging to three species—<i>P. carotovorum</i>, <i>P. versatile</i>, and <i>P. odoriferum</i>—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 <i>dnaX</i>, <i>icdA</i>, <i>mdh</i>, and <i>proA</i>, 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 <i>P. carotovorum</i>, <i>P. versatile</i>, and <i>P. odoriferum</i>, respectively. Five new haplotypes (denoted as HPc1–HPc5) were detected among cabbage strains of <i>P. carotovorum</i>, while one new haplotype was identified for both <i>P. versatile</i> (HPv1) and <i>P. odoriferum</i> (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. |
| first_indexed | 2024-03-10T23:42:09Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T23:42:09Z |
| publishDate | 2023-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-04762a5e47b74662abfb5c90125e2c632023-11-19T02:19:39ZengMDPI AGMicroorganisms2076-26072023-08-01118212210.3390/microorganisms11082122Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in SerbiaAleksandra Jelušić0Marco Scortichini1Sanja Marković2Petar Mitrović3Renata Iličić4Slaviša Stanković5Tatjana Popović Milovanović6Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, SerbiaCouncil for Agronomical Research and Economics (CREA), Research Centre for Olive, Fruit and Citrus Crops, Via di Fioranello, 52, I-00134 Roma, ItalyInstitute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, SerbiaInstitute for Field and Vegetable Crops—National Institute of the Republic of Serbia, Maksima Gorkog 30, 21000 Novi Sad, SerbiaFaculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, SerbiaFaculty of Biology, University of Belgrade, Studentski Trg 16, 11000 Belgrade, SerbiaInstitute for Plant Protection and Environment, Teodora Drajzera 9, 11040 Belgrade, SerbiaThe aim of this study was to establish a link between genetic diversity and the geographic origin of <i>Pectobacterium</i> strains belonging to three species—<i>P. carotovorum</i>, <i>P. versatile</i>, and <i>P. odoriferum</i>—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 <i>dnaX</i>, <i>icdA</i>, <i>mdh</i>, and <i>proA</i>, 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 <i>P. carotovorum</i>, <i>P. versatile</i>, and <i>P. odoriferum</i>, respectively. Five new haplotypes (denoted as HPc1–HPc5) were detected among cabbage strains of <i>P. carotovorum</i>, while one new haplotype was identified for both <i>P. versatile</i> (HPv1) and <i>P. odoriferum</i> (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.https://www.mdpi.com/2076-2607/11/8/2122phylogeographic analysisTCS haplotype network<i>Pectobacterium</i>cabbage |
| spellingShingle | Aleksandra Jelušić Marco Scortichini Sanja Marković Petar Mitrović Renata Iličić Slaviša Stanković Tatjana Popović Milovanović Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in Serbia Microorganisms phylogeographic analysis TCS haplotype network <i>Pectobacterium</i> cabbage |
| title | Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in Serbia |
| title_full | Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in Serbia |
| title_fullStr | Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in Serbia |
| title_full_unstemmed | Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in Serbia |
| title_short | Phylogeographic Analysis of Soft-Rot-Causing <i>Pectobacterium</i> spp. Strains Obtained from Cabbage in Serbia |
| title_sort | phylogeographic analysis of soft rot causing i pectobacterium i spp strains obtained from cabbage in serbia |
| topic | phylogeographic analysis TCS haplotype network <i>Pectobacterium</i> cabbage |
| url | https://www.mdpi.com/2076-2607/11/8/2122 |
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