Journal: Environmental Microbiome

Article Title: A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

doi: 10.1186/s40793-023-00473-1

Figure Lengend Snippet: Phylogenetic tree (ML) of dereplicated (97%) 16S rRNA gene sequences from Ca . Patescibacteria retrieved from NCBI genome collection (January 2022) and freshwater datasets. MAGs coming from from Baikal 1250 m, 1350 m (Illumina) and 1600 m (PacBio CCS) are blue coloured. 16S RNA genes obtained from single reads from PacBio CCS from the 1600 m sample are purple coloured. Taxonomic classification based on the Genome Taxonomy Database (GTDB) is shown: inner circle—class, outer circle—family. The Baikalibacteria are highlighted in red

Article Snippet: We included in the phylogenetic analysis sequences retrieved from the CCS assembly as well as from the lake Baikal Illumina MAGs [ , ], and the 16S rRNA gene sequences from the reference genomes described above.

Techniques:

Journal: Environmental Microbiome

Article Title: A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

doi: 10.1186/s40793-023-00473-1

Figure Lengend Snippet: a Principal component analysis of tetranucleotide frequencies of sequences affiliated to Ca. Patescibacteria. Sequences affiliated to Baikalibacteria bins are colored in green, dark and light blue, and purple, respectively. As reference, we included in the comparison the MAGs retrieved from Lake Baikal Illumina (1250 and 1350 m) and PacBio (1600 m) metagenomes. CCS reads encoding for a Baikalibacteria 16S rRNA gene (Fig. ) are colored in yellow. b Network graph showing the relationship between Lake Baikal MAGs and Baikalibacteria bins. The thickness and color of the line indicate the percentage of shared proteins (OF) and the mean amino acid identity (AAI), respectively. Interactions lower than 25% OF and/or 30% AAI were removed

Article Snippet: We included in the phylogenetic analysis sequences retrieved from the CCS assembly as well as from the lake Baikal Illumina MAGs [ , ], and the 16S rRNA gene sequences from the reference genomes described above.

Techniques:

Journal: Environmental Microbiome

Article Title: A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

doi: 10.1186/s40793-023-00473-1

Figure Lengend Snippet: a Metagenomic recruitment along two depth profiles of Lake Baikal, collected during summer and winter seasons. Only MAGs retrieved from Lake Baikal and from a study that combined 17 different freshwater samples that recruited at least 3 three reads per kilobase of genome per gigabase of metagenome (RPKGs) at 95% identity over 70% of their genome length in any of the samples are shown in the figure. The groups obtained from the binning of CCS5 reads (Baikalibacteria) are highlighted in green. b Boxplot of the metagenomic recruitment (in RPKGs, 95% identity) for each one of the CCS5 reads belonging to the four Baikalibacteria bins against two datasets: Lake Baikal metagenomes (blue boxes) and the compendium of 17 different freshwater samples (orange boxes) . For each CCS5 read in a given dataset, only the highest recruitment value was taken into account. rRNA genes were masked for the recruitment

Article Snippet: We included in the phylogenetic analysis sequences retrieved from the CCS assembly as well as from the lake Baikal Illumina MAGs [ , ], and the 16S rRNA gene sequences from the reference genomes described above.

Techniques: