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      New Penicillium and Talaromyces species from honey, pollen and nests of stingless bees

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          Abstract

          Penicillium and Talaromyces species have a worldwide distribution and are isolated from various materials and hosts, including insects and their substrates. The aim of this study was to characterize the Penicillium and Talaromyces species obtained during a survey of honey, pollen and the inside of nests of Melipona scutellaris. A total of 100 isolates were obtained during the survey and 82% of those strains belonged to Penicillium and 18% to Talaromyces. Identification of these isolates was performed based on phenotypic characters and β-tubulin and ITS sequencing. Twenty-one species were identified in Penicillium and six in Talaromyces, including seven new species. These new species were studied in detail using a polyphasic approach combining phenotypic, molecular and extrolite data. The four new Penicillium species belong to sections Sclerotiora ( Penicillium fernandesiae sp. nov., Penicillium mellis sp. nov., Penicillium meliponae sp. nov.) and Gracilenta ( Penicillium apimei sp. nov.) and the three new Talaromyces species to sections Helici ( Talaromyces pigmentosus sp. nov.), Talaromyces ( Talaromyces mycothecae sp. nov.) and Trachyspermi ( Talaromyces brasiliensis sp. nov.). The invalidly described species Penicillium echinulonalgiovense sp. nov. was also isolated during the survey and this species is validated here.

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          The online version of this article (10.1007/s10482-018-1081-1) contains supplementary material, which is available to authorized users.

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          MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

          We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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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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                Author and article information

                Contributors
                +31 (0)30-2122600 , j.houbraken@westerdijkinstitute.nl
                Journal
                Antonie Van Leeuwenhoek
                Antonie Van Leeuwenhoek
                Antonie Van Leeuwenhoek
                Springer International Publishing (Cham )
                0003-6072
                1572-9699
                13 April 2018
                13 April 2018
                2018
                : 111
                : 10
                : 1883-1912
                Affiliations
                [1 ]ISNI 0000 0004 0368 8584, GRID grid.418704.e, Westerdijk Fungal Biodiversity Institute, ; Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
                [2 ]ISNI 0000 0001 0670 7996, GRID grid.411227.3, Departamento de Micologia Prof. Chaves Batista, , Universidade Federal de Pernambuco, ; Av. Prof. Moraes Rego, s/n, Centro de Biociências, Cidade Universitária, CEP: 50670-901 Recife, PE Brazil
                [3 ]ISNI 0000 0001 2181 8870, GRID grid.5170.3, Department of Biotechnology and Biomedicine, , Technical University of Denmark, ; 2800 Kongens Lyngby, Denmark
                Article
                1081
                10.1007/s10482-018-1081-1
                6153986
                29654567
                © The Author(s) 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                Funding
                Funded by: National Council for Scientific and Technological Development (CNPq)
                Award ID: Process 201478/2015-3 – SWE
                Award Recipient :
                Funded by: Coordination for the Improvement of Higher Education Personnel (CAPES)
                Award ID: Renan Barbosa
                Award Recipient :
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                Original Paper
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                © Springer Nature Switzerland AG 2018

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