Annelid functional genomics reveal the origins of bilaterian life cycles - Supplementary Data

This GitHub repository contains the supplementary data and the custom code used in the publication cited below.

How to use and cite these files and code

All files and code are made publicly available and can be used for further research and other applications. However, if you use these resources in your work, we kindly ask you to cite our original publication.

Annelid functional genomics reveal the origins of bilaterian life cycles. Francisco M. Martín-Zamora, Yan Liang, Kero Guynes, Allan M. Carrillo-Baltodano, Billie E. Davies, Rory D. Donellan, Yongkai Tan, Giacomo Moggioli, Océane Seudre, Martin Tran, Kate Mortimer, Nicholas M. Luscombe, Andreas Hejnol, Ferdinand Marlétaz, José M. Martín-Duran. Nature 615, 105–110 (2023). https://doi.org/10.1038/s41586-022-05636-7

Author contact

• José M. Martín-Durán (senior co-author, corresponding author)
• Ferdinand Marlétaz (senior co-author, corresponding author)
• Francisco M. Martín-Zamora (co-first author)
• Yan Liang (co-first author)
• Lab website: martinduranlab.com

How to download data files

The files inside this repository are all compressed .tar.gz files stored in GitHub Large File Storage (LFS) which will need to be decompressed. To view them, select the .tar.gz file you are interested in (e.g. 05-Chordin_orthology_assignment.tar.gz), click on Download and the file will be downloaded to your device.

⚠️ Some files are very heavy and download might take time to begin: ⚠️ Be patient, they are correctly stored in GitHub Large File Storage (LFS) and your download will eventually start.

How to download code files

The code in this repository is all stored in the 00-Code folder, and can be downloaded as described above. Most scripts were built in R or Python and are therefore in .R, .py or .ipynb format, which can be visualised in your IDE of choice (e.g., RStudio, Visual Studio Code, etc.). Some of them, specially those that combine multiple steps across different programming languages or softwares called in the command line terminal, were put together in .txt or .docx files, from which the different code chunks can be copied.

We believe that the script file names and the comments in the scripts make them self-explanatory, but please do not hesitate to reach out if you have any doubts or questions.

Index of data files contents

• 01-Owenia_fusiformis_genome_assemblies.tar.gz contains the unmasked genome files in .fasta/.fa format of the two genome assemblies versions we report in the publication:
  • Scaffold_level_assembly_unmasked.fa, which is the first high-quality genome assembly that we created, upon which we have based our RNA-seq and ATAC-seq analyses, and all other analyses presented in the original publication (see above).
  • Chromosome_level_assembly_unmasked.fa, which is the chromosome-level genome assembly after HiC chromosome-scale scaffolding.
• 02-Genome_annotations.tar.gz contains the genome annotation files with all gene models in .gff3 format and the funcional annotation reports in .xlsx format for both O. fusiformis and C. teleta. Again, as described above for 01-Owenia_fusiformis_genome_assemblies.tar.gz, there are two different annotation files for O. fusiformis, which match each of the genome asembly files.
  • Capitella_teleta_genome_annotation.gff3 contains the new updated gene models of C. teleta.
  • Capitella_teleta_functional_annotation.xlsx is the functional annotation report of C. teleta.
  • Owenia_fusiformis_genome_annotation_scaffold_assembly.gff3 contains the gene models of O. fusiformis corresponding to Scaffold_level_assembly_unmasked.fa.
  • Owenia_fusiformis_genome_annotation_chromosome_assembly.gff3 contains the gene models of O. fusiformis corresponding to Chromosome_level_assembly_unmasked.fa.
  • Owenia_fusiformis_functional_annotation_scaffold_assembly.xlsx is the functional annotation report of O. fusiformis corresponding to Owenia_fusiformis_genome_annotation_scaffold_assembly.gff3.
  • Owenia_fusiformis_functional_annotation_chromosome_assembly.xlsx is the functional annotation report of O. fusiformis corresponding to Owenia_fusiformis_genome_annotation_chromosome_assembly.gff3.
• 03-Transposable_elements.tar.gz contains the repetitive and transposable elements repertoires of O. fusiformis in .fasta/.fa and .gff3 formats, which were used to mask the unmasked genome files.
  • Owenia_fusiformis_transposable_elements.fa contains the sequences of the repetitive and transposable elements of O. fusiformis.
  • Owenia_fusiformis_transposable_elements.gff3, contains the repetitive and transposable elements models of O. fusiformis, corresponding to Scaffold_level_assembly_unmasked.fa.
• 04-Orthogroups.tar.gz contains the classification by orthogroups of the non-redundant genome-based gene models of the analysed metazoan lineages in .tsv format, from which single copy orthologs can be parsed. There are two different files, which were used for different analyses of the publication:
  • Orthogroups_analysis1.tsv contains the orthogroup classification of 22 metazoan lineages. This analysis corresponds to the gene family evolution analysis used for the results reported in Fig. 1 and Extended Data Fig. 1.
  • Orthogroups_analysis1.tsv contains the orthogroup classification of 27 metazoan lineages. This analysis corresponds to the gene family evolution analysis used for the results reported in the rest of the publication.
• 05-Chordin_orthology_assignment.tar.gz contains the multiple sequence alignment (MSA) files in .fasta/.fa format used for the phylogenetic inference on Chordin sequences.
  • Chordin_mother_alignment.fa contains the "mother" MSA of 15 curated Chordin and Chordin-like protein sequences, an outgroup (human BMP endothelial regulator, BMPER), and the Chordin and Chordin-like sequences from O. fusiformis.
  • Chordin_daughter_alignment_1.fa is the "daughter" MSA #1, which contains all sequences from Chordin_mother_alignment.fa and all candidate annelid sequences that have a 10-residue or longer properly aligned fragment in the CHRD domain region of the MSA.
  • Chordin_daughter_alignment_2.fa is the "daughter" MSA #2, which contains all sequences from Chordin_mother_alignment.fa and all candidate annelid sequences that have a 10-residue or longer properly aligned fragment in any of the vWFC domain regions of the MSA.
• 06-Hox_orthology_assignment.tar.gz contains the multiple sequence alignment (MSA) files in .fasta/.fa format used for the phylogenetic inference on Hox sequences.
  • Hox_alignment1.fa contains the alignment with gaps as hyphens(-).
  • Hox_alignment2.fa contains the alignment with gaps as blank spaces ( ).
• 07-Annelid_RNAseq.tar.gz contains the gene expression matrices in transcripts-per-million (TPM) and after DESeq2 normalisation of the developmental RNA-seq time courses of O. fusiformis, C. teleta, and D. gyrociliatus containing all transcripts (i.e., all isoforms per gene model), both split by biological replicates and averaged by developmental stage. For each species:
  • <Species_name>_all_transcripts_TPM_replicates.txt is the gene expression matrix of all transcripts in TPM split by replicates.
  • <Species_name>_all_transcripts_TPM_average.txt is the gene expression matrix of all transcripts in TPM averaged by developmental stage.
  • <Species_name>_all_transcripts_DESeq2_replicates.txt is the gene expression matrix of all transcripts in DESeq2 normalised values split by replicates.
  • <Species_name>_all_transcripts_DESeq2_average.txt is the gene expression matrix of all transcripts in DESeq2 normalised values averaged by developmental stage.
• 08-Metazoan_RNAseq.tar.gz contains the gene expression matrices in transcripts-per-million (TPM) and after DESeq2 normalisation of the developmental RNA-seq time courses on the non-redundant genome-based gene models (i.e., with only one isoform, the longest, per gene model) of A. queenslandica, B. lanceolatum, C. elegans, C. teleta, C. hemisphaerica, C. gigas, D. rerio, D. gyrociliatus, D. melanogaster, N. vectensis, O. fusiformis, and S. purpuratus, both split by biological replicates and averaged by developmental stage. For each species:
  • <Species_name>_longest_isoform_TPM_replicates.txt is the gene expression matrix of the longest isoform of each gene in TPM split by replicates.
  • <Species_name>_longest_isoform_TPM_average.txt is the gene expression matrix of the longest isoform of each gene in TPM averaged by developmental stage.
  • <Species_name>_longest_isoform_DESeq2_replicates.txt is the gene expression matrix of the longest isoform of each gene in DESeq2 normalised values split by replicates.
  • <Species_name>_longest_isoform_DESeq2_average.txt is the gene expression matrix of the longest isoform of each gene in DESeq2 normalised values averaged by developmental stage.
• 09-Metazoan_Hox_expression_RNAseq.tar.gz contains the gene expression matrices as described above for 08-Metazoan_Hox_expression_RNAseq.tar.gz but with the added Hox sequences for the species whose gene models were lacking any. These are B. lanceolatum, C. teleta, D. rerio, and D. melanogaster. For each stage, the file structure is the same as above, except for the fact there is not any TPM averaged gene expression matrices.
• 10-Owenia_fusiformis_WGCNA.tar.gz and 11-Capitella_teleta_WGCNA.tar.gz contain the nodes and edges files of the full WGCNA network, as well as the nodes and edges files of the random 30% subset of the networks used for visualisation, for both O. fusiformis and C. teleta. For each .tar.gz file:
  • <Species_name>_WGCNA_nodes.txt is the nodes file of the full WGCNA network.
  • <Species_name>_WGCNA_edges.txt is the edges file of the full WGCNA network.
  • <Species_name>_WGCNA_30%_nodes.txt is the nodes file of the random subset of 30% nodes of the WGCNA network.
  • <Species_name>_WGCNA_30%_edges.txt is the edges file of the edges corresponding to the random subset of 30% nodes of the WGCNA network.
• 12-Adult_tissues_RNAseq.tar.gz contains the gene expression matrices in transcripts-per-million (TPM) and after DESeq2 normalisation of the adult tissue RNA-seq samples of O. fusiformis.
  • Adult_tissues_RNAseq_TPM.txt is the gene expression matrix in TPM.
  • Adult_tissues_RNAseq_DESeq2.txt is the gene expression matrix in DESeq2 normalised values.
• 13-Owenia_fusiformis_ATACseq_coverage.tar.gz and 14-Capitella_teleta_ATACseq_coverage.tar.gz contain the ATAC-seq stage-specific coverage files in .bigwig/.bw format for both O. fusiformis and C. teleta.
• 15-Owenia_fusiformis_ATACseq_peaks.tar.gz and 16-Capitella_teleta_ATACseq_peaks.tar.gz which contains the ATAC-seq stage-specific peak sets and the consensus peak sets in .bed format for both O. fusiformis and C. teleta.