NGS barcode sequencing in taxonomy and diagnostics, an application in “Candida” pathogenic yeasts with a metagenomic perspective

Gianluigi Cardinali; Laura Corte; Luca Roscini; Matteo Bassetti; Carlo Tascini; Joseph Mellor; Wieland Meyer; Vincent Robert; Duong Vu; Gianluigi Cardinali

doi:10.5598/imafungus.2018.09.01.07

Amanda Vaccalluzzo, Alessandra Pino, Nunziatina Russo, Maria De Angelis, Cinzia Caggia, Cinzia Lucia Randazzo (2020)
FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation. Food Microbiology 92: 103606.

DOI: 10.1016/j.fm.2020.103606

Angela Conti, Laura Corte, Debora Casagrande Pierantoni, Vincent Robert, Gianluigi Cardinali (2021)
What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes. Microorganisms 9: 299.

DOI: 10.3390/microorganisms9020299

Soumitra Paloi, Janet Jennifer Luangsa-ard, Wuttichai Mhuantong, Marc Stadler, Noppol Kobmoo (2022)
Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. Fungal Biology Reviews 42: 1.

DOI: 10.1016/j.fbr.2022.04.002

Ahmad MAHMOUDI, Boris KRYŠTUFEK, Alexander SLUDSKY, Boris V. SCHMID, Alzira M. P. DE ALMEIDA, Xu LEI, Beza RAMASINDRAZANA, Eric BERTHERAT, Aidyn YESZHANOV, Nils Chr. STENSETH, Ehsan MOSTAFAVI (2021)
Plague reservoir species throughout the world. Integrative Zoology 16: 820.

DOI: 10.1111/1749-4877.12511

Sara Windholtz, Lucie Dutilh, Marine Lucas, Julie Maupeu, Amélie Vallet-Courbin, Laura Farris, Joana Coulon, Isabelle Masneuf-Pomarède (2021)
Population Dynamics and Yeast Diversity in Early Winemaking Stages without Sulfites Revealed by Three Complementary Approaches. Applied Sciences 11: 2494.

DOI: 10.3390/app11062494

Joana Magalhães, Maria José Correia, Raquel M. Silva, Ana Cristina Esteves, Artur Alves, Ana Sofia Duarte (2022)
Molecular Techniques and Target Selection for the Identification of Candida spp. in Oral Samples. Applied Sciences 12: 9204.

DOI: 10.3390/app12189204

Kimmo Sirén, Sarah Siu Tze Mak, Ulrich Fischer, Lars Hestbjerg Hansen, M Thomas P Gilbert (2019)
Multi-omics and potential applications in wine production. Current Opinion in Biotechnology 56: 172.

DOI: 10.1016/j.copbio.2018.11.014

Robert Lücking, Paul M. Kirk, David L. Hawksworth (2018)
Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal “from the floor” to allow DNA sequences as types of names. IMA Fungus 9: 185.

DOI: 10.5598/imafungus.2018.09.01.12

Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter R. Johnston, Paul M. Kirk, Elaine Malosso, Tom W. May, Wieland Meyer, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey M. Yurkov, Ning Zhang, Conrad L. Schoch (2020)
Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?. IMA Fungus 11: .

DOI: 10.1186/s43008-020-00033-z

Claudia Colabella, Debora Casagrande Pierantoni, Laura Corte, Luca Roscini, Angela Conti, Matteo Bassetti, Carlo Tascini, Vincent Robert, Gianluigi Cardinali (2021)
Single Strain High-Depth NGS Reveals High rDNA (ITS-LSU) Variability in the Four Prevalent Pathogenic Species of the Genus Candida. Microorganisms 9: 302.

DOI: 10.3390/microorganisms9020302

Luca Roscini, Mariana Tristezza, Laura Corte, Claudia Colabella, Carla Perrotta, Patrizia Rampino, Vincent Robert, Duong Vu, Gianluigi Cardinali, Francesco Grieco (2018)
Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats. Frontiers in Microbiology 9: .

DOI: 10.3389/fmicb.2018.01687

Angela Conti, Debora Casagrande Pierantoni, Vincent Robert, Laura Corte, Gianluigi Cardinali, Michael Klutstein (2023)
MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis. Microbiology Spectrum 11: .

DOI: 10.1128/spectrum.01052-22

Nattapong Langsiri, Navaporn Worasilchai, Laszlo Irinyi, Piroon Jenjaroenpun, Thidathip Wongsurawat, Janet Jennifer Luangsa-ard, Wieland Meyer, Ariya Chindamporn (2023)
Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing. IMA Fungus 14: .

DOI: 10.1186/s43008-023-00125-6

Angela Conti, Debora Casagrande Pierantoni, Vincent Robert, Gianluigi Cardinali, Laura Corte (2021)
Homoplasy as an Auxiliary Criterion for Species Delimitation. Microorganisms 9: 273.

DOI: 10.3390/microorganisms9020273

Shiman Jiang, Yanfei Chen, Shengyi Han, Longxian Lv, Lanjuan Li (2022)
Next-Generation Sequencing Applications for the Study of Fungal Pathogens. Microorganisms 10: 1882.

DOI: 10.3390/microorganisms10101882

Debora Casagrande Pierantoni, Laura Corte, Luca Roscini, Gianluigi Cardinali (2019)
High-Throughput Rapid and Inexpensive Assay for Quantitative Determination of Low Cell-Density Yeast Cultures. Microorganisms 7: 32.

DOI: 10.3390/microorganisms7020032

Keaton Tremble, Laura M. Suz, Bryn T.M. Dentinger (2020)
Lost in translation: Population genomics and long-read sequencing reveals relaxation of concerted evolution of the ribosomal DNA cistron. Molecular Phylogenetics and Evolution 148: 106804.

DOI: 10.1016/j.ympev.2020.106804

Prassan Choudhary, Bansh Narayan Singh, Hillol Chakdar, Anil Kumar Saxena (2021)
DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance. World Journal of Microbiology and Biotechnology 37: .

DOI: 10.1007/s11274-021-03019-0

Soumitra Paloi, Wuttichai Mhuantong, Janet Jennifer Luangsa-ard, Noppol Kobmoo (2021)
Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species. Journal of Fungi 7: 767.

DOI: 10.3390/jof7090767