Additional file 1 of Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont
Creators: name: Sun, Yan
name: Wang, Minxiao
name: Cao, Lei
name: Seim, Inge
name: Zhou, Li
name: Chen, Jianwei
name: Wang, Hao
name: Zhong, Zhaoshan
name: Chen, Hao
name: Fu, Lulu
name: Li, Mengna
name: Li, Chaolun
name: Sun, Song
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology

description: Additional file 1: Supplementary Note 1. Composition of functional bacterial communities in gills of Gigantidas platifrons. Supplementary Note 2. Validation of the refined metagenome binning approach using test datasets of Escherichia coli strains. Supplementary Note 3. Assessment of the genome recovery rate of the refined genome assembly pipeline. Supplementary Note 4. Selection analysis among the genomes from the three clades. Supplementary Note 5. Population differentiation between endosymbiotic strains in different mussel groups. Supplementary Note 6. Detailed description of the functional difference between the vent and seep endosymbiont clades involved in environmental adaptation. Supplementary Note 7. Detailed description of the plasmid genes related to environmental adaptation. Supplementary Fig. 1. Overview of the refined binning pipeline in this study for the strain-level genome assembly using both Illumina and PacBio sequencing data. Supplementary Fig. 2. Taxonomic analysis of Illumina-produced sequences from 22 individual mussels. Supplementary Fig. 3. ML phylogenetic tree (left) and the pairwise ANI values (right) of the reference E. coli genomes and the assembled bins from test datasets 1 and 2 (strains with low ANI) using different binning pipelines. Supplementary Fig. 4. ML phylogenetic tree (left) and the pairwise ANI values (right) of the reference E. coli genomes and the assembled bins from test datasets 3 to 4 (strains with high ANI) using different binning pipelines. Supplementary Fig. 5. Synteny of the assembled bins obtained from E. coli test datasets 1 to 4 with their best hit reference genomes. Supplementary Fig. 6. The reads recovery rate of PacBio (a) and Illumina (b) sequencing datasets. Supplementary Fig. 7. ML phylogenetic reconstruction of endosymbiont strains based on orthologous genes conserved across the pangenome. Supplementary Fig. 8. Heatmap of pairwise average nucleotide identities (ANI) of genome assemblies in the three clades. Supplementary Fig. 9. Whole genome alignments of representative endosymbiotic genomes in the three clades. Supplementary Figure 10. Box plot of the dN/dS values for each clade obtained from each ortholog. Supplementary Figure 11. Heatmap showing the pairwise fixation index (FST) value among individual mussels collected from the hydrothermal vents (Daiyon-Yonaguni Knoll, DY; Iheya North Knoll, IN) and the methane seep (Formosa Ridge, FR). Supplementary Fig. 12. Principal coordinate analysis (PCoA) of individual mussels from the hydrothermal vents (Daiyon-Yonaguni Knoll, DY; Iheya North Knoll, IN) and the methane seep (Formosa Ridge, FR). Supplementary Fig. 13. Phylogenetic relationship of symbiont strains reconstructed with DESMAN (a) and their relative abundance among individuals from the vent (Daiyon-Yonaguni Knoll, DY; Iheya North Knoll, IN) and seep (Formosa Ridge, FR) sites (b). Supplementary Fig. 14. Box plot showing dN/dS values in the core genes and the clade-specific genes of the three clades. Supplementary Fig. 15. PCR amplification using gill DNA demonstrating the genomic variants among genomes from different clades. Supplementary Fig. 16. The assembled plasmid encoding sulfide:quinone oxidoreductase (sqr) gene.