Multigene Phylogeny Reveals <i>Haploanthostomella elaeidis</i> gen. et sp. nov. and Familial Replacement of <i>Endocalyx</i> (Xylariales, Sordariomycetes, Ascomycota)

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Abstract

During our investigation of palm fungi in Thailand, two interesting taxa from Elaeis guineensis and Metroxylon sagu (Arecaceae) were collected. Based on phylogenetic analyses of a combined dataset of ITS, LSU, rpb2, and tub2 nucleotide sequences as well as unique morphological characteristics, we introduce the new genus Haploanthostomella within Xylariales, and a new species Endocalyx metroxyli. Additionally, in our study, the genus Endocalyx is transferred to the family Cainiaceae based on its brown conidia and molecular phylogenetic evidence.

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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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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.

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Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous.

K. O'Donnell, E Cigelnik (1997)

The evolutionary history of the phytopathogenic Gibberella fujikuroi complex of Fusarium and related species was investigated by cladistic analysis of DNA sequences obtained from multiple unlinked loci. Gene phylogenies inferred from the mitochondrial small subunit (mtSSU) rDNA, nuclear 28S rDNA, and beta-tubulin gene were generally concordant, providing strong support for a fully resolved phylogeny of all biological and most morphological species. Discordance of the nuclear rDNA internal transcribed spacer 2 (ITS2) gene tree is due to paralogous or xenologous ITS2 sequences. PCR and sequence analysis demonstrated that every strain of the ingroup species tested possesses two highly divergent nonorthologous ITS2 types designated type I and type II. Only the major ITS2 type, however, is discernable when PCR products are amplified and sequenced directly with conserved primers. The minor ITS2 type was recovered using ITS2 type-specific PCR primers. Distribution of the major ITS2 type within the species lineages exhibits a homoplastic pattern of evolution, thus obscuring true phylogenetic relationships. The results suggest that the ancestral ITS2 types may have arisen following an ancient interspecific hybridization or gene duplication which occurred prior to the evolutionary radiation of the Gibberella fujikuroi complex and related species of Fusarium. The results also indicate that current morphological-based taxonomic schemes for these fungi are unnatural and a new classification is required.

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Author and article information

Contributors

Armin Mešić: Role: Academic Editor

Ivana Kušan: Role: Academic Editor

Laura Selbmann: Role: Academic Editor

Journal

Journal ID (nlm-ta): Life (Basel)

Journal ID (iso-abbrev): Life (Basel)

Journal ID (publisher-id): life

Title: Life

Publisher: MDPI

ISSN (Electronic): 2075-1729

Publication date (Electronic): 26 May 2021

Publication date Collection: June 2021

Volume: 11

Issue: 6

Electronic Location Identifier: 486

Affiliations

[1 ]CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; sirinapakonta@ 123456gmail.com (S.K.); samanthakarunarathna@ 123456gmail.com (S.C.K.); jxu@ 123456mail.kib.ac.cn (J.X.); luke.dauner1@ 123456gmail.com (L.A.P.D.)

[2 ]Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand; kdhyde3@ 123456gmail.com (K.D.H.); milan.chameera@ 123456yahoo.com (M.C.S.)

[3 ]School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand; prapassorn@ 123456mfu.ac.th

[4 ]World Agroforestry Centre, East and Central Asia, Kunming 650201, China

[5 ]Centre for Mountain Futures, Kunming Institute of Botany, Kunming 650201, China

[6 ]Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Daxuedonglu 100, Nanning 530004, China; aluthwattha@ 123456yahoo.com

[7 ]State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Daxuedonglu 100, Nanning 530004, China

[8 ]Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; saisamorn.l@ 123456cmu.ac.th

[9 ]Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand

Author notes

[* ]Correspondence: saowaluckfai@ 123456gmail.com (S.T.)

Author information

Sirinapa Konta https://orcid.org/0000-0003-1649-5223

Sasith Tharanga Aluthwattha https://orcid.org/0000-0002-9973-8165

Article

Publisher ID: life-11-00486

DOI: 10.3390/life11060486

PMC ID: 8227165

PubMed ID: 34073589

SO-VID: 5cb57d64-4ce1-4b40-b9aa-e79888d335e9

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 ( https://creativecommons.org/licenses/by/4.0/).

Multigene Phylogeny Reveals Haploanthostomella elaeidis gen. et sp. nov. and Familial Replacement of Endocalyx (Xylariales, Sordariomycetes, Ascomycota)

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Marine Life Science & Technology

Most cited references 135

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

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous.

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