Fig. 2
Phylogenomic and pan-genome analyses of reconstructed Campylobacterota MAGs from Kebrit Deep BSI. A Phylogenomic tree encompassing Sulfurimonas and Sulfurovum genomes (isolates and MAGs) made using GToTree [56] and a set of 120 bacterial marker genes. Details of the used genomes are reported in Additional file Table S1. Caminibacter mediatlanticus TB-2T (GCA 00584398) is added as an outgroup to ensure the robustness of phylogenetic affiliations. Bootstrap values are based on 1000 replicates; only values above 50% are shown at branch nodes (refer to circle size). Scale bar refers to a phylogenetic distance of 0.1 nucleotide substitutions per site. MAGs obtained in the present work (Kbt_01, Kbt_02 and Kbt_03) are reported in bold. Colours define the original environment from where the genomes were sequenced/assembled. B and C Pan-genomes of Sulfurimonas and Sulfurovum genera include the genomes of MAGs assembled from Kebrit Deep BSI, those from the less-saline Mediterranean Sea deep pools, and those from the closest related type species and MAGs identified by phylogenomic analysis (A). Pan-genome plots display gene clusters detected in Kebrit Deep MAGs Kbt_01, Kbt_02 and Kbt_03 in green, orange and light-blue, respectively, while those detected in the other reference genomes in black; light-shades of these colours indicate the absence of the gene clusters. In each plot, core gene clusters, which consist of those gene clusters present in all individuals within the group, are indicated by a blue line; Kbt_01, Kbt_02 and Kbt_03 specific gene clusters are also reported using the colour code described above. Functional annotation of gene clusters is reported in Additional File Data S6