DOI: 10.5061/dryad.ksn02v7jd
title: Metagenomic and genomic data of symbiotic bacteria from wood-boring shipworms <em>Lyrodus pedicellatus</em> and <em>Teredo bartschi</em>

description: Shipworms (Bivalvia: Teredinidae) are the most prolific wood consumers in
 marine environments. These wormlike marine bivalves digest wood using
 carbohydrate-active enzymes (CAZymes) produced by intracellular bacterial
 endosymbionts housed within their gills. Although several shipworm species
 are known to host multiple co-occurring symbiont species, the factors that
 influence symbiont community assembly, including the phylogenetic identity
 and metabolic capabilities of the symbionts, remain poorly understood. We
 sequenced gill symbiont metagenomes from multiple specimens of two
 shipworm species, Teredo bartschi (22 specimens) and Lyrodus pedicellatus
 (14 specimens), which were reared together in laboratory co-culture. From
 these metagenomes, we assembled 90 metagenome-assembled genomes (MAGs)
 representing seven distinct symbiont species. The metagenome of each host
 specimen contained between 1 and 5 symbiont species, with each including
 at least one nitrogen-fixing symbiont. Six of the seven identified
 symbiont species were found in both host species, demonstrating a
 lack of host species specificity in these symbioses. We identified
 patterns of symbiont occurrence and co-occurrence in these two hosts and
 used these to constrain the core set of CAZyme and nitrogen fixation gene
 classes necessary to support host survival. Our results indicate that, in
 these two host species, symbiont community composition reflects the
 symbionts' capabilities for carbohydrate degradation and nitrogen
 fixation, rather than strict species-specific mechanisms of host and
 symbiont sorting.
description: # Metagenomic and genomic data of symbiotic bacteria from wood-boring
 shipworms *Lyrodus pedicellatus* and *Teredo bartschi* This dataset
 supports experimental investigations into the microbiomes of wood-boring
 shipworms (*Lyrodus pedicellatus* and *Teredo bartschi*). Shipworm
 specimens were collected between 2023 and 2025 and processed for
 metagenomic sequencing. The dataset includes sample metadata,
 mitochondrial DNA–based host identification, genome quality metrics for
 bacterial symbiont isolates and metagenome-assembled genomes (MAGs),
 pairwise genome similarity metrics, predicted carbohydrate-active enzyme
 (CAZyme) functions, and genome assemblies in FASTA format. All
 supplementary files are intended to support interpretation, reuse, and
 reanalysis of the data presented in the associated publication. --- ##
 File Inventory **Supplementary_data_files.zip**\ Compressed archive
 containing three Excel datasets and a directory of FASTA genome
 assemblies. ### Contents * CheckM_isolates_results.xlsx *
 CheckM_MAGs_results.xlsx * ANI_AF_results.xlsx * Isolates_and_MAGs_fasta/
 (directory of FASTA files) * Supplementary_Table_S1_2025-09-29.pdf: Sample
 metadata for all shipworm specimens. *
 **Supplementary_Table_S2_2026-01-25.pdf: Host species identification based
 on mitochondrial DNA recovered from metagenomes.** *
 Suplementary_Table_S3_2025-09-30.pdf: Core CAZyme module subfamilies with
 predicted substrates and enzymatic activities. ### Additional
 machine-readable table files (TXT format) *
 Supplementary_Table_S1_2025-09-29.txt: Plain-text version of Supplementary
 Table S1 containing sample metadata. *
 **Supplementary_Table_S2_2026-01-25.txt: Plain-text version of
 Supplementary Table S2 containing mitochondrial DNA–based host
 identification results.** * Suplementary_Table_S3_2025-09-30.txt:
 Plain-text version of Supplementary Table S3 containing core CAZyme module
 subfamilies and predicted functions. * Supplementary_Figure_S1.pdf:
 Schematic representation of the experimental design and bioinformatic
 workflow. * Supplementary_data_description.docx: Narrative description of
 the experimental context and purpose of the dataset. --- ## Note on
 duplicate content (PDF AND TXT FORMATS) Supplementary Tables S1, S2, and
 S3 are each provided in both PDF and TXT formats. The PDF files are
 included for human readability and visual inspection, while the TXT files
 provide machine-readable versions suitable for computational reuse. The
 PDF and TXT versions contain identical underlying data, with no
 differences in content. Users may choose either format depending on their
 intended use. --- ## Detailed Description of Files and Variables ###
 Supplementary_Table_S1_2025-09-29.pdf and
 Supplementary_Table_S1_2025-09-29.txt **Sample metadata table**
 **Variables** * Sample ID: Unique identifier for each shipworm specimen.
 Type: alphanumeric string. * Host species: Morphological identification of
 the host species. Values: *Lyrodus pedicellatus* or *Teredo bartschi*. *
 Collection and processing date: Date of specimen collection and
 processing. Format: dd/mm/yyyy. **Missing values**\ No missing values
 reported. --- ### Supplementary_Table_S2_2026-01-25.pdf and
 Supplementary_Table_S2_2026-01-25.txt **Host species identification based
 on mitochondrial DNA** This table reports host species identification
 based on mitochondrial DNA sequences recovered from each sample
 metagenome. Identification is supported by pairwise sequence identity and
 recovered fraction relative to reference mitochondrial genomes and
 mitochondrial cytochrome c oxidase subunit I (COI) sequences.
 **Variables** * Sample ID: Unique identifier for each sample. Type:
 alphanumeric string. * Morphological identification: Host species
 identification based on morphology. Values: *Lyrodus pedicellatus* or
 *Teredo bartschi*. * Comparison to GenBank reference mitogenome: *L.
 pedicellatus* (OM910820).\ Pairwise nucleotide identity and recovered
 fraction of the mitochondrial genome relative to the *L. pedicellatus*
 reference.\ Format: identity/recovered portion, reported as proportions
 between 0 and 1. * Comparison to GenBank reference mitogenome: *T.
 bartschi* (OM910823).\ Pairwise nucleotide identity and recovered fraction
 of the mitochondrial genome relative to the *T. bartschi* reference.\
 Format: identity/recovered portion, reported as proportions between 0 and
 1. * Comparison to GenBank reference COI: *L. pedicellatus* (OM910820).\
 Pairwise nucleotide identity and recovered fraction of the COI gene
 relative to the *L. pedicellatus* reference.\ Format: identity/recovered
 portion, reported as proportions between 0 and 1. * Comparison to GenBank
 reference COI: *T. bartschi* (OM910823).\ Pairwise nucleotide identity and
 recovered fraction of the COI gene relative to the *T. bartschi*
 reference.\ Format: identity/recovered portion, reported as proportions
 between 0 and 1. **Interpretation key** * Values approaching 1 indicate
 high sequence identity and near-complete recovery of the corresponding
 mitochondrial region. * Consistent high identity to one species reference
 and lower identity to the alternative reference supports host species
 assignment. * Values reported as 0/0 indicate that no mitochondrial DNA
 alignment was recovered for that reference sequence. **Missing values** *
 Missing mitochondrial or COI matches are explicitly reported as 0/0 or NA,
 indicating absence of detectable alignment rather than missing data. ---
 ### Supplementary_Table_S3_2025-09-30.pdf and
 Supplementary_Table_S3_2025-09-30.txt **Core CAZyme module subfamilies and
 predicted functions** **Variables** * Subfamily name: Identifier for the
 CAZyme subfamily. Format: CAZy or dbCAN subfamily nomenclature. *
 Predicted substrate: Primary carbohydrate or polymer targeted by the
 enzyme module. * Lignocellulose component: Structural component of
 lignocellulose associated with the substrate. Values: cellulose,
 hemicellulose, lignin. * Predicted activity (EC): Enzyme Commission number
 describing the predicted catalytic activity. Format: EC number or NA. *
 Notes: Additional functional or biochemical details. * Reference source:
 Database supporting the annotation. Values include CAZy, BRENDA, and
 dbCAN. **Missing values** * NA indicates cases where no EC number is
 assigned, typically for binding-only modules or unclassified activities.
 --- ## CheckM_isolates_results.xlsx **Genome quality assessment of
 symbiont isolate assemblies** Sheet: CheckM_isolates_results **Variables**
 * Bin Id: Isolate genome identifier. * Marker lineage: CheckM marker
 lineage assignment. * Genomes: Number of genomes used in marker set
 definition. Units: count. * Markers: Number of markers in the lineage set.
 Units: count. * Marker sets: Number of marker sets. Units: count. *
 Completeness: Estimated genome completeness. Units: percent (%). *
 Contamination: Estimated genome contamination. Units: percent (%). *
 Strain heterogeneity: Estimated strain heterogeneity. Units: percent (%).
 * Genome size (bp): Assembly size. Units: base pairs (bp). * Ambiguous
 bases: Number of ambiguous bases. Units: count. * Scaffolds: Number of
 scaffolds. Units: count. * Contigs: Number of contigs. Units: count. * N50
 (scaffolds): N50 scaffold length. Units: bp. * N50 (contigs): N50 contig
 length. Units: bp. * Mean scaffold length (bp): Mean scaffold length.
 Units: bp. * Mean contig length (bp): Mean contig length. Units: bp. *
 Longest scaffold (bp): Maximum scaffold length. Units: bp. * Longest
 contig (bp): Maximum contig length. Units: bp. * GC: GC content. Units:
 percent (%). * GC std (scaffolds &gt;1 kbp): Standard deviation of GC
 content among scaffolds longer than 1 kbp. Units: percent (%). * Coding
 density: Coding density. Units: percent (%). * Translation table: Genetic
 code translation table identifier. Units: integer. * Predicted genes:
 Number of predicted genes. Units: count. * Marker occurrence distribution:
 Counts of markers occurring 0, 1, 2, 3, 4, or 5+ times. Units: count.
 Missing values: Blank or NA-like entries where CheckM metrics could not be
 computed. --- ## CheckM_MAGs_results.xlsx **Genome quality assessment of
 metagenome-assembled genomes (MAGs)** Sheet: CheckM_MAGs_results
 **Variables** * Sample: Sample identifier. * Species number: Numeric
 species or group identifier. * Host: Host species label. * Completeness:
 Estimated genome completeness. Units: percent (%). * Contamination:
 Estimated genome contamination. Units: percent (%). * Strain
 heterogeneity: Estimated strain heterogeneity. Units: percent (%). *
 Genome size (bp): Assembly size. Units: bp. * Contigs: Number of contigs.
 Units: count. * N50 (contigs): N50 contig length. Units: bp. * Mean contig
 length (bp): Mean contig length. Units: bp. * GC: GC content. Units:
 percent (%). * Marker occurrence distribution: Counts of markers occurring
 0, 1, 2, 3, 4, or 5+ times. Units: count. * Closest isolate or MAG:
 Identifier of the closest comparison genome. * ANI (1-&gt;2): Average
 Nucleotide Identity for the reported comparison. Units: percent (%). * AF
 (1-&gt;2): Alignment fraction for the reported comparison. Units: percent
 (%). Missing values: Blank or NA-like entries where metrics could not be
 computed. --- ## ANI_AF_results.xlsx **Pairwise genome similarity
 metrics** Sheet: Index Purpose: Interpretation key for the ANI_AF matrix.
 Contents: Text indicating that ANI values are reported above the diagonal
 and alignment fraction values are reported below the diagonal. Sheet:
 ANI_AF Purpose: Square matrix of pairwise genome similarity metrics.
 **Structure and variables** * Row labels: Genome IDs. * Column labels:
 Genome IDs. Matrix values: * Above diagonal: Average Nucleotide Identity
 (ANI). Units: percent (%). * Below diagonal: Alignment fraction (AF).
 Units: percent (%). * Diagonal: Self-comparisons, typically 100 percent.
 Missing values: Blank cells or NA-like entries where ANI or AF could not
 be computed. --- ## Isolates_and_MAGs_fasta **FASTA genome assemblies**
 Description: Directory containing nucleotide genome assemblies of symbiont
 isolates and metagenome-assembled genomes. **Variables** * FASTA header:
 Assembly or contig identifier. * Sequence: Nucleotide sequence composed of
 standard IUPAC DNA characters. Missing values: Not applicable. --- ##
 Experimental Workflow A schematic overview of the experimental design and
 bioinformatic workflow is provided in Supplementary_Figure_S1.pdf. The
 figure illustrates shipworm cultivation, gill dissection, DNA extraction,
 metagenomic sequencing, read processing, genome assembly, binning, quality
 control, taxonomic assignment, and downstream comparative analyses. --- ##
 Software Requirements Any standard text editor or bioinformatics software
 for FASTA files.