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      New Cladosporium Species from Normal and Galled Flowers of Lamiaceae

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          Abstract

          A series of isolates of Cladosporium spp. were recovered in the course of a cooperative study on galls formed by midges of the genus Asphondylia (Diptera, Cecidomyidae) on several species of Lamiaceae. The finding of these fungi in both normal and galled flowers was taken as an indication that they do not have a definite relationship with the midges. Moreover, identification based on DNA sequencing showed that these isolates are taxonomically heterogeneous and belong to several species which are classified in two different species complexes. Two new species, Cladosporium polonicum and Cladosporium neapolitanum, were characterized within the Cladosporium cladosporioides species complex based on strains from Poland and Italy, respectively. Evidence concerning the possible existence of additional taxa within the collective species C. cladosporioides and C. pseudocladosporioides is discussed.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          R. C. Edgar (2004)
          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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            jModelTest 2: more models, new heuristics and parallel computing.

            Diego Darriba, Guillermo Taboada, Ramón Doallo … (2012)
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              RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

              Alexandros Stamatakis (2006)
              RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak
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                Author and article information

                Contributors
                Giovanni Bubici: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Pathogens
                Journal ID (iso-abbrev): Pathogens
                Journal ID (publisher-id): pathogens
                Title: Pathogens
                Publisher: MDPI
                ISSN (Electronic): 2076-0817
                Publication date (Electronic): 19 March 2021
                Publication date Collection: March 2021
                Volume: 10
                Issue: 3
                Electronic Location Identifier: 369
                Affiliations
                [1 ]Department of Plant Protection, University of Life Sciences, 20-068 Lublin, Poland; beata.zimowska@ 123456up.lublin.pl (B.Z.); ewa.krol@ 123456up.lublin.pl (E.D.K.); agnieszka.furmanczyk@ 123456up.lublin.pl (A.F.)
                [2 ]Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; andrea.becchimanzi@ 123456unina.it
                [3 ]Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; k.bensch@ 123456wi.knaw.nl
                [4 ]Council for Agricultural Research and Economics, Research Centre for Olive, Fruit and Citrus Crops, 81100 Caserta, Italy
                Author notes
                Author information
                https://orcid.org/0000-0001-5117-0235
                https://orcid.org/0000-0002-3049-4641
                Article
                Publisher ID: pathogens-10-00369
                DOI: 10.3390/pathogens10030369
                PMC ID: 8003538
                SO-VID: 71f77919-3e04-4adf-a22b-ba6da80f39f2
                Copyright © © 2021 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 26 February 2021
                Date accepted : 17 March 2021
                Categories
                Subject: Article

                Keywords: asphondylia flower galls,cladosporium cladosporioides species complex,cladosporium neapolitanum,cladosporium polonicum,lamiaceae
                Data availability:
                Keywords: asphondylia flower galls, cladosporium cladosporioides species complex, cladosporium neapolitanum, cladosporium polonicum, lamiaceae

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