Journal article

Phylogenetic and Phylogenomic Definition of Rhizopus Species

Andrii P Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-Ling Liao, Michael T Gajdeczka, Felicia Anike, Antonina Vuek, Iryna M Anishchenko, Kerstin Voigt, G Sybren de Hoog, Matthew E Smith, Joseph Heitman, Rytas Vilgalys, Jason E Stajich

G3-GENES GENOMES GENETICS | GENETICS SOCIETY AMERICA | Published : 2018

Abstract

Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. ..

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University of Melbourne Researchers

Grants

Awarded by NSF


Awarded by NIH/NIAID R37 Merit Award


Awarded by Australian Research Council


Awarded by National Science Centre, Poland


Awarded by German Research Foundation


Awarded by NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES


Awarded by OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH


Funding Acknowledgements

This study was conducted and partially supported by the NSF-supported ZyGoLife project NSF DEB 1441715 (JES) and DEB 1441677 (MES), NIH/NIAID R37 Merit Award AI39115-20 and R01 AI50113-13 (JH), Australian Research Council grant FT130100146 (AI), and grants 2012/07/D/NZ2/04286 (AM) and 2014/15/B/NZ1/03357 (KS) from the National Science Centre, Poland as well as CRC/TransRegio 124 FungiNet from the German Research Foundation (KV). We thank Christopher Clark and Mary Catherine Aime for the R. microsporus and R. stolonifer strains from the culture collection of Louisiana State University, Piotr Mieczkowski and Ewa Patrycia Malc for the library preparation and sequencing of genomic DNA (UNC High Throughput Genomic Sequencing Facility), and Anastasia Litvintseva, Soo Chan Lee and Christina Cuomo for providing important insights and information concerning the available mucoralean genomes. We are particularly grateful to Vincent Bruno and his group for making the 16 Rhizopus and Mucor genomes available prior to publication, and to Scarlett Geunes-Boyer and Cecelia S. Walls for the improvement of the manuscript.