@article{molo_white_cornish_gell_baars_singh_carbone_isakeit_wise_woloshuk_et al._2022, title={Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control}, volume={17}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0276556}, DOI={10.1371/journal.pone.0276556}, abstractNote={Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B 1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenic A . flavus strains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A . flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A . flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A . flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.}, number={10}, journal={PLOS ONE}, author={Molo, Megan S. and White, James B. and Cornish, Vicki and Gell, Richard M. and Baars, Oliver and Singh, Rakhi and Carbone, Mary Anna and Isakeit, Thomas and Wise, Kiersten A. and Woloshuk, Charles P. and et al.}, editor={Nierman, William C.Editor}, year={2022}, month={Oct} }
 @article{carbone_white_miadlikowska_arnold_miller_magain_u'ren_lutzoni_2019, title={T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees}, volume={8}, ISSN={2576-098X}, url={http://dx.doi.org/10.1128/MRA.00328-19}, DOI={10.1128/MRA.00328-19}, abstractNote={The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata. ABSTRACT The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.}, number={29}, journal={Microbiology Resource Announcements}, publisher={American Society for Microbiology}, author={Carbone, Ignazio and White, James B. and Miadlikowska, Jolanta and Arnold, A. Elizabeth and Miller, Mark A. and Magain, Nicolas and U'Ren, Jana M. and Lutzoni, François}, editor={Cuomo, Christina A.Editor}, year={2019}, month={Jul} }
 @article{carbone_white_miadlikowska_arnold_miller_kauff_u'ren_may_lutzoni_2016, title={T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life}, volume={33}, ISSN={1367-4803 1460-2059}, url={http://dx.doi.org/10.1093/bioinformatics/btw808}, DOI={10.1093/bioinformatics/btw808}, abstractNote={Motivation: High‐quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree‐Based Alignment Selector (T‐BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single‐ and multi‐locus alignments for specific clades. Results: In its initial form, T‐BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi—Pezizomycotina (Ascomycota)—based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2). T‐BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny‐based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User‐customizable metadata can be visualized on the tree. Availability and Implementation: T‐BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu. Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. Contact: icarbon@ncsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.}, number={8}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Carbone, Ignazio and White, James B. and Miadlikowska, Jolanta and Arnold, A. Elizabeth and Miller, Mark A. and Kauff, Frank and U'Ren, Jana M. and May, Georgiana and Lutzoni, François}, year={2016}, month={Dec}, pages={btw808} }