DOI: 10.5281/zenodo.7548404
title: Appendices B to E for the Thesis: Investigating the Evolution and Ecology of Obscure Bacterial Symbioses found in Invertebrates, Ciliates and Algae

description: <strong>Appendix B1 contains all metadata for genomes assembled and genomes used, including accession numbers, CheckM scores and Gtdbtk taxonomy. You will also find supporting data for Chapter 2.</strong> <strong>Yellow tabs contain:</strong> accessions and species information for all whole genomes used brief details on hosts and environment for new genomes described in this study metadata such as N50s and genome lengths for all new genomes completeness scores and assembly levels for all genomes information on where all the published genomes were used in this study taxonomy calculations from GTDBtk <strong>Red tabs contain:</strong> Phi scores from reticulate analysis for all core genome clusters extracted from the pangenome aswell as their associated COG and KEGG functions Functional enrichment tables exploring the association of different metabolic functions with different groups of bacteria ---------------------------------------------------------------------------------------------------- <strong>Appendix C1 contains all metadata for genomes assembled and genomes used, including accession numbers and CheckM scores. You will also find raw data used to produce the figures in Chapter 3.</strong> <strong>Yellow tabs contain: </strong> S1 - Meta data tables for draft genomes examined in this study S2 - Accessions for additional genomes used <strong>Red tabs contain: </strong> S3 - AAI % similarity across Ca. Megaira used in figure 3a S4 - ANIb % Similarity across Ca. Megaira used in figure 3b S5 - KEGG ko hits S6 - KEGG module completeness used in figure 5 and 6 S7 - 16S rRNA accessions used in phylogeny Figure 2 S8 - Gene cluster presence absence matrix used in figure 3.4 and Appendix figure 1 S9 - GTDBtk results for SRA and GenBank Environmental MAGs S10 - top 10 blastp results for RiPP, NRPS and CDPS regions identified by antiSMASH ---------------------------------------------------------------------------------------------------- <strong>Appendix D1 contains all metadata for genomes assembled and genomes used, including accession numbers, CheckM scores and Gtdbtk taxonomy. You will also find raw data used to produce the figures in Chapter 4.</strong> <strong>Yellow tabs contain:</strong> S1 - Metadata for genomes assembled in this study S2 - Metadata for environmental MAGs recovered from NCBI non redundant sequence database S3 - Metadata for additional Chlamydiota genomes used <strong>Red tabs contain:</strong> S4 - AAI percentage similarity scores used to produce genera similarity networks S5 - ANIb percentage similarity scores used to produce species similarity networks S6 - CRISPRcas finder results S7 - KEGG pathway hits S8 - KEGG pathway completeness S9 - Gene cluster presence absence matrix used in figure 4.3a for Rhabdochlamydiaceae S10 - Gene cluster presence absence matrix used in figure 4.3b for Simkaniaceae ---------------------------------------------------------------------------------------------------- <strong>Appendix E1 contains screening results, environmental data extracted from climate databases and additional genome information.</strong> <strong>Yellow tabs contain:</strong> S1 - 'Ca. Tisiphia' in Anopheles plumbeus across Germany. PCR screening and geographic data S2 - additional genome accessions and metadata <strong>Red tabs contain:</strong> S3 - KEGG completeness S4 - KEGG ko_hits presence