Trends in Free‐access Genomic Data Accelerate Advances in Cyanobacteria Taxonomy

Abstract

Free access databases of DNA sequences containing microbial genetic information have changed the way scientists look at the microbial world. Currently, the NCBI database includes about 516 distinct search results for Cyanobacterial genomes distributed in a taxonomy based on a polyphasic approach. While their classification and taxonomic relationships are widely used as is, recent proposals to alter their grouping include further exploring the relationship between Cyanobacteria and Melainabacteria. Nowadays, most cyanobacteria still are named under the Botanical Code; however, there is a proposal made by the Genome Taxonomy Database (GTDB) to harmonize cyanobacteria nomenclature with the other bacteria, an initiative to standardize microbial taxonomy based on genome phylogeny, in order to contribute to an overall better phylogenetic resolution of microbiota. Furthermore, the assembly level of the genomes and their geographical origin demonstrates some trends of cyanobacteria genomics on the scientific community, such as low availability of complete genomes and underexplored sampling locations. By describing how available cyanobacterial genomes from free‐access databases fit within different taxonomic classifications, this mini‐review provides a holistic view of the current knowledge of cyanobacteria and indicates some steps towards improving our efforts to create a more cohesive and inclusive classifying system, which can be greatly improved by using large‐scale sequencing and metagenomic techniques.

Structural and Functional Genes, and Highly Repetitive Sequences Commonly Used in the Phylogeny and Species Concept of the Phylum Cyanobacteria

“…The increase of metagenomic and whole genome sequencing of cyanobacteria brings new data, which can enlighten the cyanobacterial taxonomy in the future. Nevertheless, known genomes usually represent one of the 100 genera, with more represented taxa from Nostoc Vaucher ex Bornet & Flahault, Leptolyngbya , Prochlorococcus , Synechococcus , Planktothrix Anagnostidis & Komárek, Microcystis Lemmermann and Calothrix Bornet & Flahault (Dextro et al . 2021).…”

Exploring the Relationship between Biosynthetic Gene Clusters and Constitutive Production of Mycosporine-like Amino Acids in Brazilian Cyanobacteria

“…Both strains were isolated from shaded areas and, despite having the co-linear gene cluster ( mys ABCHE), did not produce detectable concentrations of MAAs when grown under fluorescent light. This shows that sampling cyanobacteria from diverse and yet underexplored locations is relevant [ 70 ]. Searching for strains that are naturally adapted to specific environmental conditions most likely would produce high yields of specialized metabolites associated with the resilience to endure such circumstances [ 69 ].…”

Resolving Confusion Surroundingd‐Ala‐d‐Ala Ligase Catalysis in Cyanobacterial Mycosporine‐Like Amino Acid (MAA) Biosynthesis

“…[21] To redress this imbalance, cyanobacteria representing other taxonomic orders that are found in diverse and extreme environments will have to be isolated and then sequenced. [25] Nonetheless, subsequent gene and enzyme nomenclature must be consistent if sensible biochemistry and ecological information are to be inferred. A phylogenetic tree was constructed using all copies of mysD irrespective of gene cluster orientation (Figure S1).…”

“…The greatest frequency was noted in Nostocales, which arguably reflected enriched taxon sampling [21] . To redress this imbalance, cyanobacteria representing other taxonomic orders that are found in diverse and extreme environments will have to be isolated and then sequenced [25] . Nonetheless, subsequent gene and enzyme nomenclature must be consistent if sensible biochemistry and ecological information are to be inferred.…”