Incorporating molecular data in fungal systematics: a guide for aspiring researchers

By K. D. Hyde, Dhanushka Udayanga, Dimuthu Manamgoda, Leho Tedersoo, E. Larsson, Kessy Abarenkov, Yann J K Bertrand, Bengt Oxelman, Martin Hartmann, Haavard Kauserud and 3 more. 2013

83 citations recorded by the source corpus.

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/da981b4a415ad948750fe2f87c1c833e569dcba0

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Citations in the corpus

Top 50 most wanted fungi (2016, unknown): “In analogy, for sequence types found only in a single study, some sound skepticism is perhaps in place given the sequence quality-related issues involved in studies based on cloning as well as next-generation sequencing (Hyde et al. 2013; Lindahl et al. 2013; Hughes et al. 2015).”
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi (2014, background): “Submitters of newly generated fungal ITS sequences are also asked to consider previously published guidelines (96, 97).”
Applied aspects of methods to infer phylogenetic relationships amongst fungi (2020, background): “…of both morphology and molecular data developed a more trustworthy and natural classification structure that reveals true phylogenetic associations (Jeewon et al. 2002, 2003, Hyde et al. 2013, Phillips et al. 2013, 2019, Wijayawardene et al. 2014, 2016, 2020, Maharachchikumbura et al. 2015, 2016).”
Improving ITS sequence data for identification of plant pathogenic fungi (2014, background): “Another 38 sequences were annotated as ITS sequences by their submitters but were found to represent other genes and markers (notably the ribosomal small and large subunits) and were re-annotated accordingly.”
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data (2013, background): “…subterranean or otherwise inconspicuous nature of much of fungal life tends to cede little ground to sci-entiﬁc scrutiny using traditional means, and molecular (DNA) data have emerged as an integral information source in the pursuit of mycological knowledge (De Vries et al. 2011; Hyde et al. 2013).”
One stop shop: backbones trees for important phytopathogenic genera: I (2014) (2014, background): “Most of the ca. 100,000 described species of fungi are associated with plants through interactions including symbiosis, endophytism, saprotrophy and parasitism (Stajich et al. 2009; Delaye et al. 2013; Persoh 2013; Hyde et al. 2013b).”