Literature DB >> 32710773

Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences.

D Libkind1, N Čadež2, D A Opulente3,4, Q K Langdon3, C A Rosa5, J P Sampaio6, P Gonçalves6, C T Hittinger3,4, M A Lachance7.   

Abstract

In recent years, 'multi-omic' sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts. © FEMS 2020.

Entities:  

Keywords:  Guidelines; Novel species; Yeast Taxonomy

Year:  2020        PMID: 32710773     DOI: 10.1093/femsyr/foaa042

Source DB:  PubMed          Journal:  FEMS Yeast Res        ISSN: 1567-1356            Impact factor:   2.796


  8 in total

1.  What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes.

Authors:  Angela Conti; Laura Corte; Debora Casagrande Pierantoni; Vincent Robert; Gianluigi Cardinali
Journal:  Microorganisms       Date:  2021-02-02

Review 2.  Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics.

Authors:  Ashley Stengel; Kimberly M Stanke; Amanda C Quattrone; Joshua R Herr
Journal:  Front Microbiol       Date:  2022-02-17       Impact factor: 5.640

3.  Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence.

Authors:  Giselle C Martín-Hernández; Bettina Müller; Christian Brandt; Martin Hölzer; Adrian Viehweger; Volkmar Passoth
Journal:  J Fungi (Basel)       Date:  2022-03-22

Review 4.  Into the wild: new yeast genomes from natural environments and new tools for their analysis.

Authors:  D Libkind; D Peris; F A Cubillos; J L Steenwyk; D A Opulente; Q K Langdon; A Rokas; C T Hittinger
Journal:  FEMS Yeast Res       Date:  2020-03-01       Impact factor: 2.796

5.  Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021.

Authors:  Kostas Koutsoumanis; Ana Allende; Avelino Alvarez-Ordóñez; Declan Bolton; Sara Bover-Cid; Marianne Chemaly; Robert Davies; Alessandra De Cesare; Friederike Hilbert; Roland Lindqvist; Maarten Nauta; Luisa Peixe; Giuseppe Ru; Marion Simmons; Panagiotis Skandamis; Elisabetta Suffredini; Pier Sandro Cocconcelli; Pablo Salvador Fernández Escámez; Miguel Prieto-Maradona; Amparo Querol; Lolke Sijtsma; Juan Evaristo Suarez; Ingvar Sundh; Just Vlak; Fulvio Barizzone; Michaela Hempen; Lieve Herman
Journal:  EFSA J       Date:  2021-07-07

6.  The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential-Phaffia australis sp. nov. and Phaffia tasmanica sp. nov.

Authors:  Márcia David-Palma; Diego Libkind; Patrícia H Brito; Margarida Silva; Nicolás Bellora; Marco A Coelho; Joseph Heitman; Paula Gonçalves; José Paulo Sampaio
Journal:  Microorganisms       Date:  2020-10-24

7.  Nomenclatural issues concerning cultured yeasts and other fungi: why it is important to avoid unneeded name changes.

Authors:  Andrey Yurkov; Artur Alves; Feng-Yan Bai; Kyria Boundy-Mills; Pietro Buzzini; Neža Čadež; Gianluigi Cardinali; Serge Casaregola; Vishnu Chaturvedi; Valérie Collin; Jack W Fell; Victoria Girard; Marizeth Groenewald; Ferry Hagen; Chris Todd Hittinger; Aleksey V Kachalkin; Markus Kostrzewa; Vassili Kouvelis; Diego Libkind; Xinzhan Liu; Thomas Maier; Wieland Meyer; Gábor Péter; Marcin Piątek; Vincent Robert; Carlos A Rosa; Jose Paulo Sampaio; Matthias Sipiczki; Marc Stadler; Takashi Sugita; Junta Sugiyama; Hiroshi Takagi; Masako Takashima; Benedetta Turchetti; Qi-Ming Wang; Teun Boekhout
Journal:  IMA Fungus       Date:  2021-07-13       Impact factor: 3.515

Review 8.  The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks.

Authors:  Teun Boekhout; M Catherine Aime; Dominik Begerow; Toni Gabaldón; Joseph Heitman; Martin Kemler; Kantarawee Khayhan; Marc-André Lachance; Edward J Louis; Sheng Sun; Duong Vu; Andrey Yurkov
Journal:  Fungal Divers       Date:  2021-06-26       Impact factor: 20.372

  8 in total

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