Cyanobacterial Genome Sequencing, Annotation, and Bioinformatics

Whole genome sequence analysis of the filamentous Nodosilinea sp. PGN35 isolated from a mining site in Tuba, Benguet, Philippines

“…CheckM v1.1.6 (Parks et al, 2015) was used to assess the quality of assembled contigs. Since the culture was not axenic but unialgal, taxonomic binning was performed to remove contaminants (Teikari et al, 2022) using MetaBAT2 v1.7 (Kang et al, 2019), MaxBIN2 v2.2.4 (Wu et al, 2015, and CONCOCT v1.1 (Alneberg et al, 2014). The resulting bins were compared using DAS Tool v1.1.2 (Sieber et al, 2018).…”

The selectivity of 16S primers influences the results of the diversity of cyanobacteria from small water bodies

“…Our studies of benthic [10,11] and soil-inhabiting [12][13][14][15] as well as endolithic microbial communities [10,11,16,17] in mountain desert ecosystems, indicated that when using universal primers designed by Klindworth and co-authors [2] targeting the V3-V4 region of 16S rRNA primers some information concerning representative genera of cyanobacteria occurring in these communities can be lost. To our knowledge, up to now most of the primers targeting the 16S rRNA gene and the hypervariable regions have been tested to investigate cyanobacteria from pelagic habitats selecting phytoplanktonic, often bloom-forming, and potentially toxic cyanobacteria [10][11][12][13][17][18][19][20][21]. Besides studies of planktonic cyanobacteria, however, investigations of benthic cyanobacteria become more relevant due to the presence of potentially toxic cyanobacteria [22,23].…”