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    Optical mapping of the Fusarium oxysporum f. sp. melongenae genome
    (Wiley, 2022) Ates, Duygu; Altinok, Hacer H.; Tanyolac, Muhammed Bahattin
    Optical mapping approaches are widely preferred and applied in different branches of genomic studies because of their accuracy, low cost, and high efficiency. In the current study, a sequence orientation of the Fusarium oxysporum f. sp. melongenae (FOMG) genome that is deposited in GenBank National Center for Biotechnology Information under accession number MPIL00000000 was used as the reference genome, which we checked with Bionano Genomics optical mapping approaches. The optical mapping produced 103 contigs, the longest of which was 3.05 Mb. The N50 value of optical map contigs is 0.85 Mb. The sequences of the FOMG reference genome and optical map mainly match each other. Results obtained in the current study indicate that optical mapping can be used to construct complete and gapless assemblies of the FOMG genome. It also can be applied to validate a previous genome assembly.
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    Population structure and linkage disequilibrium in a large collection of Fusarium oxysporum strains analysed through iPBS markers
    (Wiley, 2019) Ates, Duygu; Altinok, Hacer H.; Ozkuru, Esin; Ferik, Filiz; Erdogmus, Semih; Can, Canan; Tanyolac, Muhammed Bahattin
    In the current study, 160 pathogenic strains of Fusarium oxysporum collected from tomato, eggplant and pepper were studied. Eighteen inter-primer binding site (iPBS)-retrotransposon primers were used, and these primers generated 205 scorable polymorphic bands. The number of polymorphic bands per primer varied between 9 and 19, with a mean of 11 bands per primer. The highest polymorphism information content (PIC) value was determined as 0.27, and the lowest was 0.05. The unweighted pair-group method with arithmetic averages (UPGMA) dendrogram including a heat map revealed that the 160 pathogenic strains of F. oxysporum were divided into two main clusters. The first cluster mainly included F. oxysporum f. sp. capsici (FOC) and F. oxysporum f. sp. melongenae (FOMG) isolates. The second cluster mainly comprised F. oxysporum f. sp. lycopersici (FOL) and F. oxysporum f. sp. radicis lycopersici (FORL) isolates. The highest percentage of loci in significant linkage disequilibrium (LD) was detected for FOL, whereas the lowest level of LD was found for FOC, and 95.2%, 99.4%, 99.1% and 97.4% of the relative kinship estimates were less than 0.4 for FOL, FOMG, FORL and FOC, respectively. LD differences were detected among formae speciales, and LD was higher in FOL as compare to FOC species. The findings of this study confirm that iPBS-retrotransposon markers are highly polymorphic at the intraspecific level in Fusarium spp.