title: MAGs
design: The qualitative and quantitative assessment of the isolated genomic DNA was conducted using a Nanodrop 1000 spectrophotometer. The concentration of isolated genomic DNA was quantified as 79.8 ng/l, having an optical density of 1.8 at A260/280. Utilizing the KAPA HyperPlus Kit (Catalogue No. 07962428001, Roche, Basel, Switzerland), the library was prepared. The Qubit 4.0 fluorometer (Catalogue No. Q33238, Thermo Fisher, Waltham, Massachusetts, USA) was used to quantify the final libraries. The DNA HS assay kit (catalogue number Q32851, Thermo Fisher, Waltham, Massachusetts, USA) was used in accordance with the manufacturer's instructions. Following the manufacturer's instructions, the very sensitive D1000 screentapes (Part No. 5067-5582, Agilent, Santa Clara, California, USA) used with the Tapestation 4150 (Agilent) were used to estimate the insert size of the library. To verify overall quality, extracted DNA was loaded onto a TBE 2% agarose gel, stained with a two-fold loading dye (Catalogue No. R0641, Thermo Fisher, Waltham, Massachusetts, USA), and the presence or absence of smearinga sign of potential contaminationwas noted. Puregene NEX-GEN DNA Ladder (Catalogue No. PG010-500DII-NV, Genetix Biotech Asia, New Delhi, India) was loaded alongside the DNA. Sequencing was performed using the Illumina MiSeq platform (Illumina, CA, USA).Adaptor sequences and poor-quality reads were eliminated using Fastp 0.24.0 (Chen et al., 2018) utilizing the parameters "-D-g-l 150" to discard duplicates, polyG tails, and reads shorter than 150 bp, accordingly. Reads aligned to the Homo sapiens and Phi X 174 genomes were eliminated using BowTie2 v2.5.4 (Langmead & Salzberg, 2012). Reads were subjected to quality assessment using FastQC v0.11.9 (bioinformatics.bbsrc.ac.uk/projects/fastqc). De novo genome assembly was performed using metaSPAdes v4.0.0 (Nurk et al., 2017). Contigs were binned using MetaBAT2 v2.17 (Kang et al., 2019), SemiBin2 v2.1.0 (Pan et al., 2023), Comebin v1.0.3 (Wang et al., 2024), and MetaDecoder v1.2 (Liu et al., 2022); bins were refined using Binette v1.1.1 (Mainguy & Hoede, 2024). The quality of the MAG was evaluated using CheckM2 v1.1.0 (Chklovski et al., 2023). The annotation of the selected genome bins was performed using BAKTA (Schwengers et al., 2021). The taxonomy of cyanobacteria and their related bacteria was determined using GTDBtk (R220) v2.4.0 (Chaumeil et al., 2022).