@article{olarte_worthington_horn_moore_singh_monacell_dorner_stone_xie_carbone_2015, title={Enhanced diversity and aflatoxigenicity in interspecific hybrids ofAspergillus flavusandAspergillus parasiticus}, volume={24}, ISSN={0962-1083}, url={http://dx.doi.org/10.1111/mec.13153}, DOI={10.1111/mec.13153}, abstractNote={AbstractAspergillus flavus and A. parasiticus are the two most important aflatoxin‐producing fungi responsible for the contamination of agricultural commodities worldwide. Both species are heterothallic and undergo sexual reproduction in laboratory crosses. Here we examine the possibility of interspecific matings between A. flavus and A. parasiticus. These species can be distinguished morphologically and genetically, as well as by their mycotoxin profiles. Aspergillus flavus produces both B aflatoxins and cyclopiazonic acid (CPA), B aflatoxins or CPA alone, or neither mycotoxin; Aspergillus parasiticus produces B and G aflatoxins or the aflatoxin precursor O‐methylsterigmatocystin, but not CPA. Only four of forty‐five attempted interspecific crosses between opposite mating types of A. flavus and A. parasiticus were fertile and produced viable ascospores. Single ascospore strains from each cross were shown to be recombinant hybrids using multilocus genotyping and array comparative genome hybridization. Conidia of parents and their hybrid progeny were haploid and predominantly monokaryons and dikaryons based on flow cytometry. Multilocus phylogenetic inference showed that experimental hybrid progeny were grouped with naturally occurring A. flavus L strain and A. parasiticus. Higher total aflatoxin concentrations in some F1 progeny strains compared to midpoint parent aflatoxin levels indicate synergism in aflatoxin production; moreover, three progeny strains synthesized G aflatoxins that were not produced by the parents, and there was evidence of allopolyploidization in one strain. These results suggest that hybridization is an important diversifying force resulting in the genesis of novel toxin profiles in these agriculturally important fungi.}, number={8}, journal={Molecular Ecology}, publisher={Wiley}, author={Olarte, Rodrigo A. and Worthington, Carolyn J. and Horn, Bruce W. and Moore, Geromy G. and Singh, Rakhi and Monacell, James T. and Dorner, Joe W. and Stone, Eric A. and Xie, De-Yu and Carbone, Ignazio}, year={2015}, month={Apr}, pages={1889–1909} }
 @article{monacell_carbone_2014, title={Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics}, volume={30}, ISSN={1460-2059 1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btu055}, DOI={10.1093/bioinformatics/btu055}, abstractNote={AbstractSummary: Previously we developed the stand-alone SNAP Workbench toolkit that integrated a wide array of bioinformatics tools for phylogenetic and population genetic analyses. We have now developed a web-based portal front-end, using the Mobyle portal framework, which executes all of the programs available in the stand-alone SNAP Workbench toolkit on a high-performance Linux cluster. Additionally, we have expanded the selection of programs to over 189 tools, including population genetic, genome assembly and analysis tools, as well as metagenomic and large-scale phylogenetic analyses. The Mobyle SNAP Workbench web portal allows end users to (i) execute and manage otherwise complex command-line programs, (ii) launch multiple exploratory analyses of parameter-rich and computationally intensive methods and (iii) track the sequence of steps and parameters that were used to perform a specific analysis. Analysis pipelines or workflows for population genetic, metagenomic and genome assembly provide automation of data conversion, analysis and graphical visualization for biological inference.Availability: The Mobyle SNAP Workbench portal is freely available online at http://snap.hpc.ncsu.edu/. The XMLs can be downloaded at http://carbonelab.org/system/files/snap_xmls.tgz. Each XML provides links to help files, online documentation and sample data.Supplementary information:  Supplementary data are available at Bioinformatics online.}, number={10}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Monacell, James T. and Carbone, Ignazio}, year={2014}, month={Jan}, pages={1488–1490} }
 @article{jana m. u'ren_riddle_monacell_carbone_miadlikowska_arnold_2014, title={Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi}, volume={14}, ISSN={["1755-0998"]}, DOI={10.1111/1755-0998.12252}, abstractNote={AbstractNext‐generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next‐generation methods can lead to difficult‐to‐detect errors in estimating fungal community richness, distributions and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design and various quality‐control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first contrast 454 data sets generated contemporaneously from subsets of the same plant and lichen tissues that were stored in CTAB buffer, dried in silica gel or freshly frozen prior to DNA extraction. We show that storage in silica gel markedly limits the recovery of sequence data and yields a small fraction of the diversity observed by the other two methods. Using lichen mycobiont sequences as internal positive controls, we next show that despite careful filtering of raw reads and utilization of current best‐practice OTU clustering methods, homopolymer errors in sequences representing rare taxa artificially increased estimates of richness c. 15‐fold in a model data set. Third, we show that inferences regarding endolichenic diversity can be improved using a novel primer that reduces amplification of the mycobiont. Together, our results provide a rationale for selecting tissue treatment regimes prior to DNA extraction, demonstrate the efficacy of reducing mycobiont amplification in studies of the fungal microbiomes of lichen thalli and highlight the difficulties in differentiating true information about fungal biodiversity from methodological artefacts.}, number={5}, journal={MOLECULAR ECOLOGY RESOURCES}, author={Jana M. U'Ren and Riddle, Jakob M. and Monacell, James T. and Carbone, Ignazio and Miadlikowska, Jolanta and Arnold, A. Elizabeth}, year={2014}, month={Sep}, pages={1032–1048} }
 @article{olarte_horn_dorner_monacell_singh_stone_carbone_2012, title={Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis}, volume={21}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294x.2011.05398.x}, abstractNote={AbstractAspergillus flavus is the major producer of carcinogenic aflatoxins (AFs) in crops worldwide. Natural populations of A. flavus show tremendous variation in AF production, some of which can be attributed to environmental conditions, differential regulation of the AF biosynthetic pathway and deletions or loss‐of‐function mutations in the AF gene cluster. Understanding the evolutionary processes that generate genetic diversity in A. flavus may also explain quantitative differences in aflatoxigenicity. Several population studies using multilocus genealogical approaches provide indirect evidence of recombination in the genome and specifically in the AF gene cluster. More recently, A. flavus has been shown to be functionally heterothallic and capable of sexual reproduction in laboratory crosses. In the present study, we characterize the progeny from nine A. flavus crosses using toxin phenotype assays, DNA sequence‐based markers and array comparative genome hybridization. We show high AF heritability linked to genetic variation in the AF gene cluster, as well as recombination through the independent assortment of chromosomes and through crossing over within the AF cluster that coincides with inferred recombination blocks and hotspots in natural populations. Moreover, the vertical transmission of cryptic alleles indicates that while an A. flavus deletion strain is predominantly homokaryotic, it may harbour AF cluster genes at a low copy number. Results from experimental matings indicate that sexual recombination is driving genetic and functional hyperdiversity in A. flavus. The results of this study have significant implications for managing AF contamination of crops and for improving biocontrol strategies using nonaflatoxigenic strains of A. flavus.}, number={6}, journal={MOLECULAR ECOLOGY}, author={Olarte, Rodrigo A. and Horn, Bruce W. and Dorner, Joe W. and Monacell, James T. and Singh, Rakhi and Stone, Eric A. and Carbone, Ignazio}, year={2012}, month={Mar}, pages={1453–1476} }
 @article{abbas_weaver_horn_carbone_monacell_shier_2011, title={Selection of Aspergillus flavus isolates for biological control of aflatoxins in corn}, volume={30}, ISSN={["1556-9551"]}, DOI={10.3109/15569543.2011.591539}, abstractNote={The fungus Aspergillus flavus is responsible for producing carcinogenic mycotoxins, the aflatoxins, on corn (maize) and other crops. An additional harmful toxin, cyclopiazonic acid, is produced by some isolates of A. flavus. Several A. flavus strains that do not produce one or both of these mycotoxins are being used in biological control to competitively exclude the toxin-producing strains from the agroecosystem, particularly from seeds, grain and other marketable commodities. Three well-studied non-aflatoxigenic strains, including two that are commercially available, have been compared in side-by-side field trials. The results of that study, together with a growing understanding of A. flavus ecology and new genetic insights, are guiding the selection of biocontrol strains and influencing crop management decisions for safe and sustainable production.}, number={2-3}, journal={TOXIN REVIEWS}, author={Abbas, Hamed K. and Weaver, Mark A. and Horn, Bruce W. and Carbone, Ignazio and Monacell, James T. and Shier, W. Thomas}, year={2011}, pages={59–70} }