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      Cryptic diversity found in Didymellaceae from Australian native legumes

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          Ascochyta koolunga ( Didymellaceae , Pleosporales ) was first described in 2009 (as Phoma koolunga ) and identified as the causal agent of Ascochyta blight of Pisum sativum (field pea) in South Australia. Since then A. koolunga has not been reported anywhere else in the world, and its origins and occurrence on other legume ( Fabaceae ) species remains unknown. Blight and leaf spot diseases of Australian native, pasture and naturalised legumes were studied to investigate a possible native origin of A. koolunga .

          Ascochyta koolunga was not detected on native, naturalised or pasture legumes that had leaf spot symptoms, in any of the studied regions in southern Australia, and only one isolate was recovered from P. sativum . However, we isolated five novel species in the Didymellaceae from leaf spots of Australian native legumes from commercial field pea regions throughout southern Australia. The novel species were classified on the basis of morphology and phylogenetic analyses of the internal transcribed spacer region and part of the RNA polymerase II subunit B gene region. Three of these species, Nothophoma garlbiwalawarda sp. nov., Nothophoma naiawu sp. nov. and Nothophoma ngayawang sp. nov., were isolated from Senna artemisioides . The other species described here are Epicoccum djirangnandiri sp. nov. from Swainsona galegifolia and Neodidymelliopsis tinkyukuku sp. nov. from Hardenbergia violacea . In addition, we report three new host-pathogen associations in Australia, namely Didymella pinodes on S. artemisioides and Vicia cracca , and D. lethalis on Lathyrus tingitanus . This is also the first report of Didymella prosopidis in Australia.

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          MrBayes 3: Bayesian phylogenetic inference under mixed models.

          MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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             T.J White,  T. Bruns,  S. Lee (1990)
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              Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

              Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the β-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa.

                Author and article information

                Pensoft Publishers
                08 February 2021
                : 78
                : 1-20
                [1 ] School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, SA 5005, Australia The University of Adelaide Adelaide Australia
                [2 ] Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, QLD 4102, Australia Royal Botanic Gardens and Domain Trust Sydney Australia
                [3 ] Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Mrs Macquaries Rd, Sydney, NSW 2000, Australia Department of Agriculture and Fisheries, Ecosciences Precinct Dutton Park Australia
                [4 ] Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia University of Southern Queensland Toowoomba Australia
                Author notes
                Corresponding author: Elizabeth C. Keirnan ( elizabeth.keirnan@ 123456adelaide.edu.au )

                Academic editor: I. Schmitt

                Elizabeth C. Keirnan, Yu Pei Tan, Matthew H. Laurence, Allison A. Mertin, Edward C. Y. Liew, Brett A. Summerell, Roger G. Shivas

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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