Fig. 2

The Tibetan Plateau Lake Microbiome (TPLM) atlas. A Phylogenetic tree for 2422 species-like OTUs. The maximum likelihood tree is built based on GTDB alignments of 120 and 122 single-copy genes universally distributed in bacteria and archaea, respectively, using IQ-Tree with LG + I + G model. Archaeal and bacterial trees are combined manually and branch length is ignored for better visualization. The major phyla and classes of Proteobacteria are marked with different colors. The blue-to-red heatmaps represent estimated genome size (defined as assembled genome size divided by the sum of genome completeness and contamination) and GC content. The strip charts from inner to outer circle represent number of genomes affiliated with a species-like OTU, number of known BGCs, and number of novel BGCs, respectively. B Quality of the 8271 TPLM MAGs. C Recruitment rates of metagenomic sequencing reads against the 8271 TPLM MAGs. The p values of < 0.001 based on Welch’s t-test between different types of lakes are colored in red. Abbreviation: n.s. not significant, *** p < 0.001. D Taxonomic assignment and novelty. The taxonomic assignment is performed using GTDB-Tk with the database version of RS202. The phylogenetic diversity (PD) gain is represented as the difference between the total branch lengths of GTDB reference genomes (RS202) with and without the addition of the 8271 TPLM MAGs. E Rarefaction curve of species-like OTUs detected in lake samples. F Proportion of species-like OTUs annotated in GTDB database at each taxonomic level