The genomic DNA of HK05 was extracted using a DNA Extraction minikit (Invitrogen) following the manufacturer’s instructions, and sequenced using an Illumina Hiseq 2000 sequencing system (Novogene Company). The sequences obtained were assembled using Spades with k-mer 55 and 77 (72 (link)). To remove possible contigs from heterotrophic bacteria, those ≥2 kb were binned using MyCC (73 (link)). The quality of the obtained genomes was evaluated using CheckM (70 (link)), and the genome identified as being affiliated with Cyanobacteria was retained for subsequent analysis. The YX04-3 genome was obtained from the NCBI database (accession number: RHLE00000000.1).
To annotate the YX04-3 and HK05 genomes, the genome sequences of both were then submitted to the RAST Server for open reading frame (ORF) prediction (74 (link)). The predicted ORFs and amino acid sequences were annotated using eggNOG-mapper v2 (75 (link)), BlastKOALA (76 (link)) and the nr database with default settings (Data set S2).
We compared genomes of YX04-3 and HK05, as well as other strains of clade III and CB4. The distribution of genes involved in salinity adaption, channel proteins synthesis, and nitrogen and phosphorus metabolisms were compared.
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