Browsing by Author "Zhou, Xin"

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    Data supporting "Single-cell detection of copy number changes reveals dynamic mechanisms of adaptation to antifungals in Candida albicans"
    (2024-07-10) Zhou, Xin; Hilk, Audrey; Solis, Norma V; Scott, Nancy; Beach, Annette; Soisangwan, Natthapon; Billings, Clara L; Burrack, Laura S; Filler, Scott G; Selmecki, Anna; Selmecki@umn.edu; Anna Selmecki; University of Minnesota Selmecki lab
    Genomic copy number changes are associated with antifungal drug resistance and virulence across diverse fungal pathogens. Despite the high prevalence of both gain and loss events, the rate and dynamics of these genomic changes in the presence of antifungal drugs is not known for any organism. We optimized a dual-fluorescent reporter system in the diploid pathogen Candida albicans to quantify copy number variation (CNV) and loss of heterozygosity (LOH) at the single cell level with flow cytometry. We followed the rate and dynamics of CNV and LOH at two distinct genomic locations during parallel evolution experiments in the presence and absence of antifungal drugs in vitro and in a murine model of infection. Copy number changes were rapid and dynamic during adaptation to three different concentrations of the azole drug fluconazole. The fluorescent reporters revealed competing sub-populations with distinct genotypes in the drug-evolved lineages. Extensive whole genome sequencing identified recurrent genotypes that cause increased competitive fitness in the presence of antifungal drug. Specifically, at low concentrations of drug, chromosome 3 (Chr3) LOH frequently arose and led to significantly increased competitive fitness. In contrast, at high drug concentrations, Chr3 and Chr6 aneuploidy arose together, and these concurrent aneuploidies conferred multi-azole tolerance. In the murine model, copy number changes were only detected in isolates recovered from mice treated with fluconazole, and included whole-genome duplication events resulting in polyploidy. This study provides the first quantitative evidence for the incredible speed at which diverse genotypes arise and undergo dynamic population-level fluctuations during adaptation to antifungal drugs in vitro and in vivo.  
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    DNA barcode data confirm new species and reveal cryptic diversity in Chilean Smicridea (Smicridea) (Trichoptera:Hydropsychidae)
    (The North American Benthological Society, 2010) Pauls, Steffen U.; Blahnik, Roger J.; Zhou, Xin; Wardwell, C. Taylor; Holzenthal, Ralph W.
    Mitochondrial deoxyribonucleic acid (mtDNA) sequence data have been both heralded and scrutinized for their ability or lack thereof to discriminate among species for identification (DNA barcoding) or description (DNA taxonomy). Few studies have systematically examined the ability of mtDNA from the DNA barcode region (658 base pair fragment of the 59 terminus of the mitochondrial cytochrome c oxidase I gene) to distinguish species based on range-wide sampling of specimens from closely related species. Here we examined the utility of DNA barcode data for delimiting species, associating life stages, and as a potential genetic marker for phylogeographic studies by analyzing a rangewide sample of closely related Chilean representatives of the caddisfly genus Smicridea subgenus Smicridea. Our data revealed the existence of 7 deeply diverged, previously unrecognized lineages and confirmed the existence of 2 new species: Smicridea (S.) patinae, new species and Smicridea (S.) lourditae, new species. Based on our current taxonomic evaluation, we considered the other 5 lineages to be cryptic species. The DNA barcode data proved useful in delimiting species within Chilean Smicridea (Smicridea) and were suitable for life-stage associations. The data also contained sufficient intraspecific variation to make the DNA barcode a candidate locus for widespread application in phylogeographic studies.
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    The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life
    (The Royal Society Publishing, 2016) Zhou, Xin; Frandsen, Paul B.; Holzenthal, Ralph W.; Beet, Clare R.; Bennett, Kristi R.; Blahnik, Roger J.; Bonada, Nu´ria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V.; Collins, Gemma E.; deWaard, Jeremy; Dean, John; Flint, Oliver S. Jr; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D.; Kondratieff, Boris C.; Malicky, Hans; Milton, Megan A.; Morinie`re, Je´roˆme; Morse, John C.; Ngera Mwangi, Francois; Pauls, Steffen U.; Razo Gonzalez, Marı´a; Rinne, Aki; Robinson, Jason L.; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A.; Zamora-Munoz, Carmen; Ziesmann, Tanja; Kjer, Karl M.
    DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life’s species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’.