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      Illuminating type collections of nectriaceous fungi in Saccardo’s fungarium

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          Abstract

          Specimens of Nectria spp. and Nectriella rufofusca were obtained from the fungarium of Pier Andrea Saccardo, and investigated via a morphological and molecular approach based on MiSeq technology. ITS1 and ITS2 sequences were successfully obtained from 24 specimens identified as ‘ Nectria’ sensu Saccardo (including 20 types) and from the type specimen of Nectriella rufofusca. For Nectria ambigua, N. radians and N. tjibodensis only the ITS1 sequence was recovered. On the basis of morphological and molecular analyses new nomenclatural combinations for Nectria albofimbriata, N. ambigua, N. ambigua var. pallens, N. granuligera, N. peziza subsp. reyesiana, N. radians, N. squamuligera, N. tjibodensis and new synonymies for N. congesta, N. flageoletiana, N. phyllostachydis, N. sordescens and N. tjibodensis var. crebrior are proposed. Furthermore, the current classification is confirmed for Nectria coronata, N. cyanostoma, N. dolichospora, N. illudens, N. leucotricha, N. mantuana, N. raripila and Nectriella rufofusca. This is the first time that these more than 100-yr-old specimens are subjected to molecular analysis, thereby providing important new DNA sequence data authentic for these names.

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              QIIME allows analysis of high-throughput community sequencing data.

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                Author and article information

                Journal
                Persoonia
                Persoonia
                Persoonia
                Persoonia : Molecular Phylogeny and Evolution of Fungi
                Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures
                0031-5850
                1878-9080
                23 November 2020
                December 2020
                : 45
                : 221-249
                Affiliations
                [1 ]Botanical Garden, University of Padova, Via Orto Botanico, 15, 35123 Padova, Italy.
                [2 ]Department of Life Sciences and Systems Biology, University of Torino, Viale P.A. Mattioli, 25, 10125 Torino, Italy;
                [3 ]Institute for Sustainable Plant Protection (IPSP-SS Torino), C.N.R., Viale P.A. Mattioli, 25, 10125 Torino, Italy.
                [4 ]Department of Biology, University of Padova, Via Ugo Bassi, 58b, 35121 Padova, Italy;
                Author notes
                corresponding author e-mail: alfredo.vizzini@ 123456unito.it .
                corresponding author e-mail: barbara.baldan@ 123456unipd.it .
                Article
                10.3767/persoonia.2020.45.09
                8375352
                34456378
                99e87e43-5c14-4609-b449-8d57d1691a11
                © 2019–2020 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute

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                History
                : 25 June 2020
                : 21 September 2020
                Categories
                Research Article

                Plant science & Botany
                ancient dna,ascomycota,hypocreales,illumina,ribosomal sequences,sordariomycetes
                Plant science & Botany
                ancient dna, ascomycota, hypocreales, illumina, ribosomal sequences, sordariomycetes

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