@article{rogers_koehler_crouch_cubeta_leblanc_2022, title={Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata}, volume={22}, ISSN={["2730-7182"]}, DOI={10.1186/s12862-022-02035-4}, abstractNote={Boxwood blight disease caused by Calonectria henricotiae and C. pseudonaviculata is of ecological and economic significance in cultivated and native ecosystems worldwide. Prior research has focused on understanding the population genetic and genomic diversity of C. henricotiae and C. pseudonaviculata, but gene family evolution in the context of host adaptation, plant pathogenesis, and trophic lifestyle is poorly understood. This study applied bioinformatic and phylogenetic methods to examine gene family evolution in C. henricotiae, C. pseudonaviculata and 22 related fungi in the Nectriaceae that vary in pathogenic and saprobic (apathogenic) lifestyles.A total of 19,750 gene families were identified in the 24 genomes, of which 422 were rapidly evolving. Among the six Calonectria species, C. henricotiae and C. pseudonaviculata were the only species to experience high levels of rapid contraction of pathogenesis-related gene families (89% and 78%, respectively). In contrast, saprobic species Calonectria multiphialidica and C. naviculata, two of the closest known relatives of C. henricotiae and C. pseudonaviculata, showed rapid expansion of pathogenesis-related gene families.Our results provide novel insight into gene family evolution within C. henricotiae and C. pseudonaviculata and suggest gene family contraction may have contributed to limited host-range expansion of these pathogens within the plant family Buxaceae.}, number={1}, journal={BMC ECOLOGY AND EVOLUTION}, author={Rogers, Layne W. and Koehler, Alyssa M. and Crouch, Jo Anne and Cubeta, Marc A. and LeBlanc, Nicholas R.}, year={2022}, month={Jun} }
 @article{rogers_koehler_2021, title={Nondestructive Sampling to Monitor Macrophomina phaseolina Root Colonization in Overwintering Stevia}, volume={22}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-10-20-0092-BR}, abstractNote={Macrophomina phaseolina is a soilborne fungal pathogen in the family Botryosphaeriaceae. Microsclerotia of M. phaseolina were first observed at the base of overwintering stevia stems in North Carolina in spring 2016. Previous studies utilized destructive sampling methods to monitor M. phaseolina in stevia fields; however, these methods are not feasible for long-term monitoring of disease in a perennial system. In the current study, nondestructive root soil-core sampling was conducted during overwintering months, from October 2018 to January 2020, to monitor M. phaseolina root colonization in stevia in Rocky Mount, NC. Two-inch-diameter soil cores were collected through the root zone, and fresh weight of roots was recorded for each soil core. M. phaseolina recovery was evaluated by examining mycelial growth from roots plated onto potato dextrose agar. There was no significant effect of sample weight on M. phaseolina across all dates, but there was one date for which sample weight had a significant effect on recovery (P = 0.01; α = 0.05). For both recovery and sample weight, sampling date was a significant predictor (P = 1.68e-5 and P = 0.0389, respectively; α = 0.05). Weather and climate data revealed that dates with no M. phaseolina recovery had lowest mean air and soil temperatures and the greatest number of days below freezing in the month prior to sampling. In separate sampling years, October sampling dates had the highest recovery of M. phaseolina. Future field trials should determine if October samplings can predict survival and vigor of reemerging stevia plants.}, number={2}, journal={PLANT HEALTH PROGRESS}, author={Rogers, Layne W. and Koehler, Alyssa M.}, year={2021}, pages={151–153} }
 @article{koehler_larkin_rogers_carbone_cubeta_shew_2019, title={Identification and characterization of Septoria steviae as the causal agent of Septoria leaf spot disease of stevia in North Carolina}, volume={111}, ISSN={0027-5514 1557-2536}, url={http://dx.doi.org/10.1080/00275514.2019.1584503}, DOI={10.1080/00275514.2019.1584503}, abstractNote={Stevia (Stevia rebaudiana) is an emerging perennial crop in the southeastern United States. A Septoria leaf spot disease of stevia was first identified on field plantings in Japan in 1978. The pathogen was named Septoria steviae based on a morphological characterization. In 2015, a species of Septoria with morphological characters of S. steviae was isolated from field and greenhouse-grown stevia plants with leaf spot symptoms in North Carolina. In this study, 12 isolates obtained from diseased stevia plants in 2015 and 2016 were characterized and compared with reference strains of S. steviae. Comparisons were based on conidial and pycnidial morphology and multilocus sequence analysis of actin (ACT), β-tubulin (BT), calmodulin (CAL), nuc rDNA internal transcribed spacers (ITS1-5.8S-ITS2 = ITS), nuc rDNA 28S subunit (28S), RNA polymerase II second largest subunit (RPB2), and translation elongation factor-1α (TEF1). Measurements of conidia and pycnidia from symptomatic field leaves and 12 pure cultures grown on nutrient medium were consistent with those previously reported for ex-type strains of S. steviae. North Carolina strains formed a well-supported monophyletic group with ex-type strains of S. steviae. This study represents the first genetic characterization of S. steviae in the United States and provides an experimental framework to elucidate the genetic diversity and disease ecology of field populations of S. steviae.}, number={3}, journal={Mycologia}, publisher={Informa UK Limited}, author={Koehler, Alyssa M. and Larkin, Maximo T. and Rogers, Layne W. and Carbone, Ignazio and Cubeta, Marc A. and Shew, H. David}, year={2019}, month={Apr}, pages={456–465} }