DOI: 10.5281/zenodo.14984093
title: Supplemental data for "The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with reduced posterior tagma"

description: # List of files on Zenodo


Data accompanying the manuscript have been uploaded on Zenodo (10.5281/zenodo.14185694). Here we

present a brief description of each file and put them in meaningful groups.


## referenced supplement


(Cited) supplementary material from the manuscript. For more information, please refer to the figure/table legends and the supplementary file descriptions.


- suppl-fig1-genomescope.png

- suppl-fig2-abdA_araneae.png

- suppl-fig3-paralog_content.svg

- suppl-fig4-genomic_context.png

- suppl-fig5-alignment.pdf

- suppl-fig6-Plit_COI-alignment_distances.pdf


- suppl-file1-hox_tree.pdf

- suppl-file2-hro_tree.pdf

- suppl-file3-irx_tree.pdf

- suppl-file4-sine_tree.pdf

- suppl-file5-nk_tree.pdf

- suppl-file6-dbx.png

- suppl-file7-gene_analysis.zip


- suppl-table1-data_overview.csv

- suppl-table2-genome_progress.csv

- suppl-table3-Pycnognonum_microRNAs.csv

- suppl-table4-named_genes.csv

- suppl-table5-abdA.csv

- suppl-table6-r2_g3735-Alignment-HitTable.csv

- suppl-table7-isoseq.csv

- suppl-table8-chelicerate_repeat_content.csv

- suppl-table9-arthropod_genomes.csv

- suppl-table10-arthropod_repeat_content.csv

- suppl-table11-chelicerate_genomes.csv

- suppl-table12-self_synteny.csv


- unref-table-mapping_rates.tsv: back-mapping rates of the various genomic and transcriptomic resources to the draft genome.


## figures


- figs.zip: archive of raw and processed figures for the manuscript in full resolution


## analysis


### genomic context


The broader arthropod/chelicerate context for the _P. litorale_ genome assembly.


- araneae.tsv: repeat makeup of published chelicerate assemblies

- arthropoda.tsv: genome assembly statistics for arthropod genomes. From NCBI Genomes.

- modern_taxids.txt: list of taxonomic IDs for species; made to be submitted to NCBI Taxonomy.

- tax_report.txt: the full taxonomic report for each query species. Contains tax IDs for the entire lineage.

- total_repeats.tsv: total repeat content of published chelicerate genomes.


### Homeobox genes


Files concerning the Homeobox gene cluster analysis. Each folder (hro, irx, nkx, sine) contains the

candidate sequences from Aase-Remedios et al., the P. litorale sequences that matched, the multiple

sequence alignment, the trimmed alignment, and the tree files.


Additionally, the hox/ folder contains the analysis done for the AbdA gene, with searches performed

against the de-novo assembled transcriptomes (.m8 files).


Finally, the r2_g3735/ folder contains the analysis of the r2_3735 gene model, which is found in the

Hox cluster area on the P. litorale genome. Sequence searches against NCBI nr and the developmental

transcriptomes show that the gene has putative homologs in other taxa and is expressed throughout

development.


## processed (intermediate) data


### 00-kmer-jellyfish.zip


k-mer spectra analysis with GenomeScope and GenomeScope2.0


### 00-seq-qc.zip


quality control output for raw sequencing data (e.g. FastQC output)


### 01-assembly


- assembly_graph.gfa: Flye output

- assembly_graph.gv: Flye output

- assembly_info.txt: Flye output

- assembly.fasta: Flye output

- backmap.hifi.sort.bam.cov-hist.pdf: coverage histogram of the back-mapped PacBio data

- backmap.ont.sort.bam.cov-hist.pdf: coverage histogram of the back-mapped ONT data

- BUSCO.arthropoda_odb10.txt: BUSCO completeness report (arthropoda_odb10)

- BUSCO.metazoa_odb10.txt: BUSCO completeness report (metazoa_odb10)

- flye.log: Flye assembler log

- quast_report.pdf: assembly QC


### 02-scaffold


`yahs` output files:


- asm_hic.sorted.bam

- flye-yahs.fa

- yahs.out_scaffolds_final.agp

- yahs.out_scaffolds_final.fa.hic

- yahs.out_scaffolds_final.fa.assembly


Juicebox (manual curating) results:


- yahs.out_scaffolds_final.fa.review.assembly

- 02-flye-yahs-juicebox.fa


GAP `sort_scaffolds` pipeline outputs


- 03-flye-yahs-juicebox-merge.fasta

- plit_q_0_50000_0.5FracBest_unseen_scaffolds.txt

- plit_q_0_50000_0.5FracBest_insertion_stats.tsv

- plit_q_0_50000_0.5FracBest_appended_scaffolds.tsv

- plit_q_0_50000_0.5FracBest_inserted_scaffolds.tsv


### 03-contamination


Refer to the [contamination analysis](https://github.com/galicae/plit-genome/blob/main/04-contam/README.md) for details.


Decontaminating the draft genome from non-metazoan scaffolds:


- plit_q_0_50000_0.5FracBest_output_filtered.fasta: input draft genome

- contam_tax.m8: Alignment results of UniRef90 against draft genome (MMseqs2)

- scaffolds_taxonomic_distribution.tsv: summary of contam_tax.m8; number of genes from each taxonomic level per scaffold.

- scaffolds_taxonomic_distribution_collapsed_vir.tsv: scaffolds with predominantly viral hits

- scaffolds_taxonomic_distribution_suspect.tsv: scaffolds whose genes are <90% metazoan


Checking for widespread _Metridium_ contamination:


- primary_mq30.txt: list of high-quality mapping reads (presumptive "metridial")

- metridium_scaffolds.txt_summary: no. of presumptive _Metridium_ reads per draft scaffold

- metridium_scaffolds.txt: filtered SAM file with all high-quality "_Metridium_" hits on draft scaffolds

- metridium_contigs.sam_summary: no. of presumptive _Metridium_ reads per Flye contig


### 04-annotation


Repeat analysis with RepeatModeler/RepeatMasker:


- draft.fasta.tbl: output of RepeatModeler in tabular form

- pb.sam.flagstats: summary of mapping the repeat families to the PacBio data.

- pycno-families.fa: output of RepeatModeler - the sequences of the _P. litorale_ repeat families

- draft.fasta.out.gff: output of RepeatModeler - repeat locations on the draft genome


Protein coding gene annotation:


- annot-01-isoseq.gff: GFF file with the gene models proposed using Iso-seq isoforms

- annot-01-braker.gff: GFF file with the gene models proposed from round 1 of BRAKER3 using developmental transcriptomes

- annot-02-braker.gff3: GFF file with the gene models proposed from round 2 of BRAKER3, using developmental transcriptome reads that weren't used in round 1

- annot-03-denovo.gff3: GFF file with the gene models proposed from the de novo transcriptomes

- deep_denovo_assemblies.zip: the de-novo assembled transcriptomes from the deeply sequenced developmental time points. Also available on ENA.


tRNAscan output


- trnascan.bed

- trnascan.out

- trnascan.fasta

- trnascan.stats


MirMachine output


- Pli_september.PRE.gff: MirMachine output with permissive threshold

- Pli_september.PRE-1.gff: MirMachine output with strict threshold

- Pli_september.PRE.fasta: predicted miRNA sequences


## Results


- draft_softmasked.fasta: draft genome with repetitive regions softmasked

- draft.fasta: draft genome fasta

- hox.gff3: the position of the Hox genes in GFF3 form.

- merged_sorted_named_dedup_flagged.gff3: protein-coding gene models from all rounds of annotation after deduplication

- transcripts.fa: TransDecoder-extracted putative transcripts

- transcripts.fa.transdecoder.pep: TransDecoder predicted peptides

- out.emapper.annotations: EggNOG-mapper functional annotation for the predicted peptides

- out.emapper.best.annotations: filtered EggNOG-mapper annotation; best hit per gene kept

- miRNA.fasta: FASTA sequences of predicted miRNAs

- miRNA.lenient.gff: GFF of miRNA positions (permissive MirMachine cutoff)

- miRNA.strict.gff: GFF of miRNA positions (strict MirMachine cutoff)