DOI: 10.5061/dryad.4tmpg4fqm
title: Data from: Symbiont replacement and subsequent genome erosion reshape a dual obligate aphid symbiosis

description: Many insects rely on obligate microbial symbioses, often involving
 multiple partners. Although symbiont replacement is well-documented, how
 newly acquired and resident obligate symbionts adapt after such events
 remains unclear. Here, we investigate the dual obligate symbiosis of the
 aphid Lachnus tropicalis, where an ancestral Serratia lineage was replaced
 by a newly acquired another Serratia lineage while the primary symbiont
 Buchnera remained. Our metagenomic sequencing yielded complete genomes of
 Buchnera (0.42 Mb) and Serratia (2.8 Mb), revealing developing metabolic
 complementarity. Although the Serratia genome retained abundant gene sets
 for amino acid synthesis, it also contained pseudogenes in leucine and
 methionine pathways, which would be compensated for by Buchnera or the
 host. Comparison with L. roboris, which harbors the ancestral Serratia
 lineage, showed that the newly acquired Serratia in L. tropicalis exhibits
 identical tissue localization and vertical transmission pattern,
 suggesting the smooth succession of the prior’s microniche. Notably,
 Buchnera in L. tropicalis exhibited a slightly more degenerated genome
 than its counterpart in L. roboris, indicating that symbiont replacement
 can accelerate gene loss even in ancient symbionts. Overall, our findings
 provide new insights into the dynamics of novel mutualism establishment
 and highlight symbiont replacement as a driver of host-symbiont
 co-evolution.
description: # Dataset: Symbiont replacement and subsequent genome erosion reshape a
 dual obligate aphid symbiosis (Dryad_upload_files.zip) DOI:
 [https://doi.org/10.5061/dryad.4tmpg4fqm](https://doi.org/10.5061/dryad.4tmpg4fqm) Manuscript Information Journal: Proceedings of the Royal Society B (RSPB) Manuscript Title: Symbiont replacement and subsequent genome erosion reshape a dual obligate aphid symbiosis Authors: Tomonari Nozaki, Yuuki Kobayashi, Mika Ikeda, Shuji Shigenobu ### 1. Data Accessibility and External Repositories All datasets generated and analyzed in this study are publicly available. Raw sequencing reads,including 16S rRNA amplicon sequences (DRR709987–DRR709998), Nanopore long reads (DRR718948), and Illumina short reads (DRR718949), have been deposited in the DDBJ Sequence Read Archive (DRA) under BioProject ID PRJDB35790. The primary raw sequencing data are further associated with BioSample ID: SAMD01601843. The assembled genome sequences of Buchnera aphidicola isolate Lt-NIBB (BioSample ID: SAMD01609681, Accession numbers: AP043953 and AP043954) and Serratia symbiotica isolate Lt-NIBB (BioSample ID: SAMD01609682, Accession numbers: AP043955-AP043957) from L. tropicalis are also available in the DDBJ/GenBank/ENA database under BioProject ID PRJDB35790. This Dryad repository contains the secondary and processed data, and source files required to reproduce the figures and supplementary materials. ### 2. Dryad Data Contents This uploaded folder contains several subfolders corresponding to the figures presented in the main manuscript and supplementary information. Files within each folder are named according to the corresponding figure or table panel (e.g., "Figure 1", "Figure2a" and "Table S4") for ease of navigation. All files are provided in machine-readable formats for full reproducibility. * Figure1_Amplicon_sequencing: Microbial community composition data (csv) used for Figure 1. The files were manually modified from original data generated by QIIME2 (version 2020.8) and QIIME2 view ([https://view.qiime2.org/](https://view.qiime2.org/)). * Figure2a_genome_visualization: Image data (svg) from proksee ([https://proksee.ca/](https://proksee.ca/)) used to generate the genome structure visualization map in Figure 2a. * Figure3_FISH_bacteriome: High-resolution raw TIFF images showing tissue localization via FISH (Fluorescence in situ hybridization) in the bacteriome used for Figure3. ".tif" are raw microscopic images generated by FV1000 Fluoview software. "_mod.tif" are modified images with adjusted brightness/contrast by ImageJ for visualization in the manuscript. ".txt" are Metadata files automatically generated by the microscope software (Fluoview), containing acquisition parameters. * Figure4_S10_S11_FISH_embryo: High-resolution raw TIFF images illustrating the vertical transmission patterns in embryos used for Figure 4, S10, and S11. ".tif" are raw microscopic images generated by FV1000 Fluoview software. "_mod.tif" are modified images with adjusted brightness/contrast by ImageJ for visualization in the manuscript. ".txt" are Metadata files automatically generated by the microscope software (Fluoview), containing acquisition parameters. * Figure5_Orthofinder_result: OrthoFinder v3.1.0 input (faa) and output files (TSV/TXT) used for ortholog clustering and functional gene analysis (Figure 5b). * FigureS1_S2_phylogeny: Sequences (fasta) and phylogenetic analysis files (mtsx) generated by MEGA X used for generating Figures S1 and S2. * FigureS3_Blobplot_output Raw output data (txt) and image files (pdf/png) from the Blobplot analysis for genome quality assessment for Figure S3. * FigureS4_TableS4-S12_genomic_data DFAST annotation files for genomic comparisons for Figure S4, Table S4-S12. Each DFAST output file contains annotation (.gbk, gff), cds (fna), features (.tsv), genome (.fna), protein (.faa), pseudogene list (.tsv), rna (.fna) and statistics (.txt). COG_analysis_DFAST_summary.sxl is a summary file that is manually produced by the authors. * FigureS5_S6_Phylogenomic_analysis_data Alignments and supporting data for phylogenomic analysis with iqtree (Figure S5 and S6). The analysis was conducted with GToTree v1.8.14 and IQ-TREE v2.4.0. * FigureS13_Genomic_data DFAST annotation files for genomic comparisons used for Figure S13. Each DFAST output file contains annotation (.gbk, gff), cds (fna), features (.tsv), genome (.fna), protein (.faa), pseudogene list (.tsv), rna (.fna) and statistics (.txt). ### 3. Analysis Protocols Detailed descriptions of the analysis protocols, including command lines, specific software versions, and parameter settings (e.g., for QIIME2 or phylogenetic inference), are fully documented in the Supplementary Information (SI) section of the submitted manuscript.