Microbial taxonomy with DNA sequence data as nomenclatural type: how far should we go?
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
Taxonomy aims to recognize all living beings and understand their evolutionary relationships. As the most basic discipline, taxonomy is of benefit to other disciplines via facilitating scientific communication; it also uses data from other disciplines as evidence to delimit the circumscription of taxa. At the moment, whatever discipline the data comes from, the nomenclatural type of a species or infraspecific taxon is required to be a real material. However, high-throughput sequencing technology and bioinformatics tools have revealed innumerable microorganisms that may possess crucial ecological functions but are unculturable under the current methodology from various environments. Accordingly, an independent code, viz. SeqCode using whole-genome sequence data as the nomenclatural type for prokaryotes regardless of cultivability was newly initiated. SeqCode definitely will facilitate scientific communication about innumerable unculturable prokaryotes. However, how to deal with at least five concerns, viz. A. Republication of known species, B. Restriction of bioresource utilization, C. Publication of species with hard-to-assemble genomes, D. Advancement of genome sequencing and assembling technology and E. Balance between biosecurity and data sharing is crucial for further utilizing SeqCode. Compared with prokaryotes, the debate as to whether accept DNA sequence data as a category of nomenclatural type for fungi or not is ongoing. In summary, the old taxonomy needs to embrace new technology as it has over the ages. However, it should find a suitable methodology to face the emendation of codes and adjust the method continuously.