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      Diversity of Backusella ( Mucoromycotina) in south-eastern Australia revealed through polyphasic taxonomy

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          Abstract

          Here we explore the diversity of one morphologically distinguishable genus in the Mucoromycotina, Backusella, in south-eastern Australia. We isolated more than 200 strains from locations across the states of Victoria and Tasmania. Characterization of these strains using a combination of approaches including morphology, sucrose utilization and whole genome sequencing for 13 strains, revealed 10 new species. The genetic basis for interspecies variation in sucrose utilization was found to be the presence of a gene encoding an invertase enzyme. The genus Backusella is revised and a new key for species identification produced. Given that we have more than doubled the number of species in this genus, this work demonstrates that there may be considerable undiscovered species diversity in the early diverging fungal lineages.

          Citation: Urquhart AS, Douch JK, Heafield TA, et al. 2021. Diversity of Backusella (Mucoromycotina) in south-eastern Australia revealed through polyphasic taxonomy. Persoonia 46: 1–25. https://doi.org/10.3767/persoonia.2021.46.01.

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          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

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            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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              BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

              Felipe A. Simão, Robert Waterhouse, Panagiotis Ioannidis … (2015)
              Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Persoonia
                Journal ID (iso-abbrev): Persoonia
                Journal ID (publisher-id): Persoonia
                Title: Persoonia : Molecular Phylogeny and Evolution of Fungi
                Publisher: Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures
                ISSN (Print): 0031-5850
                ISSN (Electronic): 1878-9080
                Publication date (Electronic): 21 September 2020
                Publication date (Print): June 2021
                Volume: 46
                Pages: 1-25
                Affiliations
                [1 ]School of BioSciences, the University of Melbourne, VIC 3010, Australia
                [2 ]Centre for Agriculture and Bioscience International (CABI), Wallingford, Oxfordshire, OX10 8DE, UK.
                Author notes
                corresponding author e-mail: alexander.idnurm@ 123456unimelb.edu.au .
                Article
                DOI: 10.3767/persoonia.2021.46.01
                PMC ID: 9311390
                SO-VID: 8351d6d7-194a-4356-b014-f956137c0e53
                Copyright © © 2020-2021 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute
                License:

                You are free to share - to copy, distribute and transmit the work, under the following conditions:

                Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work).

                Non-commercial: You may not use this work for commercial purposes.

                No derivative works: You may not alter, transform, or build upon this work.

                For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights.

                History
                Date received : 5 June 2020
                Date accepted : 17 August 2020
                Categories
                Subject: Research Article

                ScienceOpen disciplines: Plant science & Botany
                Keywords: backusella,genome sequencing,invertase,mucorales,new taxa,polyphasic taxonomy,zygospore
                Data availability:
                ScienceOpen disciplines: Plant science & Botany
                Keywords: backusella, genome sequencing, invertase, mucorales, new taxa, polyphasic taxonomy, zygospore

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