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      Three new species of Rhytidhysteron (Dothideomycetes, Ascomycota) from Mexico

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          Abstract

          The genus Rhytidhysteron is characterised by forming navicular to apothecial hysterothecia, exposing the green, yellow, orange, red, vinaceous or black colours of the hymenium which generally releases pigments in the presence of KOH. The exciple is smooth or striated, the asci bitunicate and ascospores have 1–5 transverse septa. To date, twenty-six Rhytidhysteron species have been described from the Tropics. The present study aims to describe three new species in the Neotropics of Mexico based on molecular methods and morphological features. Illustrations and a taxonomic key are provided for all known species of this genus. Rhytidhysteron cozumelense from the Isla Cozumel Biosphere Reserve, R. esperanzae from the Sierra Juárez, Oaxaca and R. mesophilum from the Sierra Madre Oriental, Hidalgo are described as new species. With the present study, the number of species of Rhytidhysteron known from Mexico is now increased to eight.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          Kazutaka Katoh, Daron Standley (2013)
          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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            MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

            K Katoh (2002)
            A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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              AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

              T.J White, T. Bruns, S. Lee … (1990)
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                Author and article information

                Contributors
                Aurora Cobos-Villagrán:
                ORCID: https://orcid.org/0000-0003-2649-9906
                Role: InvestigationRole: ValidationRole: Writing - original draftRole: Writing - review and editing
                Ricardo Valenzuela: Role: ConceptualizationRole: Funding acquisitionRole: ResourcesRole: SupervisionRole: Validation
                César Hernández-Rodríguez: Role: Funding acquisitionRole: ResourcesRole: SupervisionRole: Validation
                Rosa Paulina Calvillo-Medina: Role: InvestigationRole: MethodologyRole: ResourcesRole: Validation
                Lourdes Villa-Tanaca: Role: Funding acquisitionRole: SupervisionRole: Validation
                Luz Elena Mateo-Cid:
                ORCID: https://orcid.org/0000-0001-7585-4826
                Role: Funding acquisitionRole: SupervisionRole: Validation
                Abigail Pérez-Valdespino: Role: Funding acquisitionRole: SupervisionRole: Validation
                César Ramiro Martínez-González: Role: Formal analysisRole: MethodologyRole: Software
                Tania Raymundo: Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: SupervisionRole: ValidationRole: Writing - original draft
                Journal
                Journal ID (nlm-ta): MycoKeys
                Journal ID (iso-abbrev): MycoKeys
                Journal ID (publisher-id): 11
                Journal ID (index): urn:lsid:arphahub.com:pub:C004A564-9D6A-5F9F-B058-6A3815DFE9C3
                Title: MycoKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-4057
                ISSN (Electronic): 1314-4049
                Publication date Collection: 2021
                Publication date (Electronic): 14 September 2021
                Volume: 83
                Pages: 123-144
                Affiliations
                [1 ] Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Laboratorio de Micología, Prolongación de Carpio y Plan de Ayala s/n, Mexico City 11340, Mexico Instituto Politécnico Nacional Mexico City Mexico
                [2 ] Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Laboratorio Experimental de Bacterias y Levaduras, Prolongación de Carpio y Plan de Ayala s/n, Mexico City 11340, Mexico Universidad Autónoma de Querétaro Querétaro Mexico
                [3 ] Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Laboratorio de Ficología, Prolongación de Carpio y Plan de Ayala s/n, Mexico City 11340, Mexico Universidad Autónoma Chapingo Estado de México Mexico
                [4 ] Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Laboratorio de Ingeniería Genética, Prolongación de Carpio y Plan de Ayala s/n, Mexico City 11340, Mexico Instituto Politécnico Nacional Mexico City Mexico
                [5 ] Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas s/n, Querétaro 76010, Mexico Universidad Autónoma de Querétaro Querétaro Mexico
                [6 ] Universidad Autónoma Chapingo, Departamento de Fitotecnia, Instituto de Horticultura, Km 38.5 Carretera Federal México-Texcoco, Texcoco, Estado de México 56230, Mexico Universidad Autónoma Chapingo Estado de México Mexico
                Author notes
                Corresponding author: Tania Raymundo ( traymundoo@ 123456ipn.mx )

                Academic editor: Cecile Gueidan

                Author information
                https://orcid.org/0000-0003-2649-9906
                https://orcid.org/0000-0001-7585-4826
                Article
                Publisher ID: 68582
                DOI: 10.3897/mycokeys.83.68582
                PMC ID: 8455505
                SO-VID: 1b679820-9c08-4f49-8357-eabe4d9dbf5b
                Copyright © Aurora Cobos-Villagrán, Ricardo Valenzuela, César Hernández-Rodríguez, Rosa Paulina Calvillo-Medina, Lourdes Villa-Tanaca, Luz Elena Mateo-Cid, Abigail Pérez-Valdespino, César Ramiro Martínez-González, Tania Raymundo
                License:

                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.

                History
                Date received : 12 May 2021
                Date accepted : 09 August 2021
                Funding
                Instituto Politécnico Nacional
                Categories
                Subject: Review Article
                Subject: Hysteriaceae
                Subject: Identification Key
                Subject: Molecular Systematics
                Subject: Phylogeny
                Subject: Taxonomy
                Subject: Americas
                Subject: Mexico
                Subject: North America

                Keywords: hysteriaceae , hysteriales ,neotropic,phylogeny, taxonomy
                Data availability:
                Keywords: hysteriaceae , hysteriales , neotropic, phylogeny, taxonomy

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