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    A novel approach for in vitro fungicide screening and the sensitivity of Monilinia populations from peach orchards in Turkey to respiratory inhibitor fungicides
    (Elsevier Ltd, 2021) Durak, Muhammed R.; Arslan, Kübra; Sılan, Ece; Yıldız, Gözde; Özkılınç, Hilal
    Brown rot caused by Monilinia fructicola and M. laxa can result in considerable losses in peach production worldwide. Respiratory Inhibitors (RIs) have been used to control the disease in Turkey and worldwide. However, resistance against RIs may have been developing in Monilinia populations in Turkey. The sensitivity level of the total of 128 isolates of Monilinia fructicola and M. laxa from peach fruits in Turkey were tested against certain RIs: azoxystrobin, boscalid, and commercially used signum (26,7% boscalid, 6,7% pyraclostrobin). Fungal growth from both mycelia and conidia was evaluated as fungicide response phenotypes. A new approach was developed to define the sensitivity levels of the isolates. The mean IC50 values of each fungicide on representative collection from each species were used as discriminatory doses in view of both phenotypes. The whole collection was scanned at discriminatory doses and the relative growth (RG) of each isolate was obtained. The distribution of RG data sets in the quantile ranges was considered to define sensitivity levels of the isolates against each fungicide. Resistance levels for mycelial and conidial growth assays varied within and between the species against the three RIs. According to the pairwise correlation analyses between responses of the species to the fungicides, the significant correlation indicating a cross-resistance was only found between boscalid and signum on conidial growth assays for M. fructicola. This study represents in vitro fungicide responses of a large population of Monilinia pathogens from peach in Turkey for the first time which will help to reconsider disease control strategies and suggests a fungicide sensitivity definition be used in all in vitro fungicide assays as a common and comparable strategy at the global stage.
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    Genome-Wide Discovery of Structural Variants Reveals Distinct Variant Dynamics for Two Closely Related Monilinia Species
    (Oxford University Press, 2023) Durak, Muhammed R.; Özkılınç, Hilal
    Structural variants (SVs) are variants with sizes bigger than 50 bp and capable of changing the size, copy number, location, orientation, and sequence content of genomic DNA. Although these variants have been proven to be extensive and involved in many evolutionary processes along the tree of life, there is still insufficient information on many fungal plant pathogens. In this study, the extent of SVs, as well as single-nucleotide polymorphisms (SNPs), has been determined for two prominent species of the Monilinia genus (the causal agents of brown rot disease in pome and stone fruits): Monilinia fructicola and Monilinia laxa for the first time. The genomes of M. fructicola were found to be more variant-rich in contrast to M. laxa based on the reference-based variant calling (with a total number of 266.618 and 190.599 SNPs and 1,540 and 918 SVs, respectively). The extent, as well as distribution of SVs, presented high conservation within the species and high diversity between the species. Investigation of potential functional effects of characterized variants revealed high potential relevance of SVs. Moreover, the detailed characterization of copy number variations (CNVs) for each isolate revealed that around 0.67% of M. fructicola genomes and 2.06% of M. laxa genomes are copy number variables. The variant catalog as well as distinct variant dynamics within and between the species presented in this study opens doors for many further research questions.