U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska
Date of this Version
12-1-2021
Citation
Microbiology Resource Announcements Volume 10 Issue 48 e00784-21
Abstract
In a recent letter to the editor, Houbraken et al. (23) provide a series of recommendations to the microbiological community to prevent the taxonomic misidentification of genome-sequenced fungal strains. In the era of genomics and bioinformatics, postulating that 1 nucleotide (nt) within a gene can “correctly” identify a species does not seem plausible. However, the authors of the letter call this the “calmodulin barcode,” meaning nucleotide substitutions within a 506-nt region of the calmodulin gene (1). After the evolutionarily conserved rRNA (18S rRNA, internal transcribed spacer [ITS], 28S rRNA) and RNA polymerase II (2–4) showed no differences between Aspergillus flavus S- and Lmorphotypes, attention shifted toward the calmodulin gene. Thus, without sequencing 18S rRNA, 28S rRNA, or the largest RNA polymerase II subunit, at least 34 new species of Aspergillus were named by Houbraken, Frisvad, Visagie, and coworkers (1, 5, 6). However, in a phylogenetic tree of 152 Aspergillus section Flavi isolates using the calmodulin 506- nt region, 40 Aspergillus minisclerotigenes isolates had only two nucleotide substitutions in common, namely, 100C.A and 269A.G, both of which are silent mutations (Fig. 1). However, only 269A.G discriminates A. minisclerotigenes from A. flavus, since 100C.A is present in three A. flavus isolates (GenBank accession numbers MK451387, MK451365, and MG517986) identified by the authors of the letter. We all agree that species identification is important; paradoxically, the calmodulin barcode assigns species based on a single-nucleotide polymorphism (SNP), while there are between 133,000 and 179,000 SNPs within A. flavus S- and L-morphotypes, respectively (7). Another limitation of Aspergillus taxonomy is the chemotypes resulting from 30 genes in the aflatoxin biosynthesis gene cluster (ABC) (8), e.g., A. flavus produces B-aflatoxins and Aspergillus parasiticus produces B and G types (9). Despite that a single nucleotide change in one ABC gene can prevent aflatoxin production (10), the inheritance of the ABC is favored by environmental pressure (11), and Aspergillus spp. are not physically or reproductively isolated; intraspecies and interspecies crosses can result in gain of function, e.g., G-type aflatoxin production (9, 12, 13). Hence, a new species named by one author of the letter was later reversed to its initial name by the same author because of the chemotype, i.e., A. flavus S-morphotype to Aspergillus parvisclerotigenus (14) and back to A. flavus (6). Other groups utilized the calmodulin gene and a single deletion in the ABC to name three new Aspergillus species (15, 16).
Comments
U.S. government work