Lessons Learned: the Importance of Biological Curation.

Abstract

Proper species identification of sequenced fungal isolates or strains is imperative for the interpretation of genomics data. Through this letter (1), and through another recently published research note (2), it has come to our attention that one of the isolates presented in our previous publication (3) was misidentified. The presumptive Aspergillus parasiticus isolate NRRL 2999 has been shown to be an Aspergillus flavus isolate, a clonal derivative of A. flavus NRRL 3357 (2). In our recent publication presenting two new reference genomes for A. flavus (4), we performed a phylogenomics analysis of several publicly available Aspergillus assemblies and noted the sequence similarity between A. flavus NRRL 3357 and A. parasiticus NRRL 2999. We also noted a close relationship between A. flavus WRRL 1519 and A. oryzae RIB40 and that A. oryzae RIB40 grouped among A. flavus isolates, not as an outgroup. Based on these analyses, we concluded that the A. flavus species is polyphyletic. The revelation that NRRL 2999 is indeed an A. flavus isolate clonal to NRRL 3357 (2) does point toward A. flavus as a distinct species from A. parasiticus but does not change the conclusion of the potential polyphyletic nature of A. flavus based on the position of A. oryzae in the analysis (4). All additional conclusions were based on phylogenetic relationships defined within the scope of the manuscript (4) and were therefore independent of species labels.