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. 2024 Mar 5;40(4):122.
doi: 10.1007/s11274-024-03914-2.

Evaluation of molecular typing methods for some scab-causing Streptomyces strains from Turkey

Kenan Karagoz  1 , Fatih Dadasoglu  2 , Burak Alaylar  3 , Recep Kotan  2
Affiliations

Evaluation of molecular typing methods for some scab-causing Streptomyces strains from Turkey

Kenan Karagoz et al. World J Microbiol Biotechnol. .

Abstract

This study was conducted for identifying phylogenetic relationships between 15 scab-causing Streptomyces species including S. bottropensis, S. europaeiscabiei, S. scabiei, S. stelliscabiei and, other 11 Streptomyces sp. All of the strains were originally isolated from symptomatic potatoes in Erzurum Province, The Eastern Anatolia Region of Turkey. Some morphological and biochemical properties of the strains were defined in our former research. Then, 16 s rRNA regions of them were sequenced. After the sequence data assembly, phylogenetic analyzes were performed. The phylogenetic analyses revealed that the strains are involved in the same major group and, substantially similar to reference strains. Additionally, some subgroup formations were also recorded. Moreover, Repetitive element-based PCR (Rep-PCR), Enterobacterial repetitive intergenic consensus (ERIC-PCR), and BOX-PCR fingerprinting molecular typing methods were used for as molecular typing methods. According to our knowledge, this is the first report on phylogenetic relationships of scab-causing Streptomyces species from Turkey. However, the identification of most pathogenic strains remained at the species level.

Keywords: 16S rRNA; BOX-PCR Streptomyces; Common-scab; ERIC-PCR; Phylogeny; Rep-PCR.

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Conflict of interest statement

The authors declare that they have no conflict of interest in the publication.

Figures

Fig. 1
Fig. 1
Phylogenetic tree of scab-causing Streptomyces spp. based on 16S rRNA regions sequences. (GenBank® accession numbers are presented in brackets)
Fig. 2
Fig. 2
Dendrogram generated from ERIC-PCR banding pattern of 15 Streptomyces strains. The similarity analysis was performed with Bray–Curtis and UPGMA method
Fig. 3
Fig. 3
Dendrogram generated from REP-PCR banding pattern of 15 Streptomyces strains. The similarity analysis was performed with Bray–Curtis and UPGMA method
Fig. 4
Fig. 4
Dendrogram generated from BOX-PCR banding pattern of 15 Streptomyces strains. The similarity analysis was performed with Bray–Curtis and UPGMA method
Fig. 5
Fig. 5
ERIC-PCR band profiles of Streptomyces strains with ERIC 1R and ERIC 2 primers. Lanes 1, Marker; 2, KS196; 3, KS464; 4, KS176; 5, KS573; 6, KS613; 7, KS227; 8, KS177; 9, KS308; 10, KS541; 11, KS606; 12, KS229; 13, KS465; 14, KS525; 15, KS542; 16, KS561
Fig. 6
Fig. 6
REP-PCR band profiles of Streptomyces strains with REP 1R and REP 2 primers. Lanes 1, Marker; 2, KS196; 3, KS464; 4, KS176; 5, KS573; 6, KS613; 7, KS227; 8, KS177; 9, KS308; 10, KS541; 11, KS606; 12, KS229; 13, KS465; 14, KS525; 15, KS542; 16, KS561
Fig. 7
Fig. 7
BOX-PCR band profiles of Streptomyces strains with BOXA1R primer. Lanes 1, Marker; 2, KS196; 3, KS464; 4, KS176; 5, KS573; 6, KS613; 7, KS227; 8, KS177; 9, KS308; 10, KS541; 11, KS606; 12, KS229; 13, KS465; 14, KS525; 15, KS542; 16, KS561
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