DOI: 10.5281/zenodo.14362378
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


Supplementary material from the manuscript.


- suppl-fig1-alignment.pdf

- suppl-fig2-genomescope.png

- suppl-fig3-abdA_araneae.png

- suppl-fig4-genomic_context.png


- suppl-table1-data_overview.tsv

- suppl-table2-Plit_COI-alignment_distances.pdf

- suppl-table3-isoseq.tsv

- suppl-table4-genome_progress.tsv

- suppl-table5-abdA.tsv

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

- suppl-table7-chelicerate_genomes.tsv

- suppl-table8-arthropod_repeat_content.tsv

- suppl-table9-chelicerate_repeat_content.tsv

- suppl-table10-Pycnognonum_microRNAs.xlsx


- suppl-file1-araneae_abdA.fasta

- suppl-file2-arthropod_genomes.tsv


- unref-table-mapping_rates.tsv


## 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. Files used/generated by the [genomic_context](https://github.com/galicae/plit-genome/blob/main/07-analysis/genomic_context.ipynb) notebook.


- 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.


### Hox genes


Files concerning the Hox gene cluster analysis.


- Plit_HoxGenes.fasta: putative Hox gene sequences for P. litorale

- putative_hox-Alignment-HitTable.csv:

- araneae_abdA.fasta: arachnid abdA sequences from NCBI

- araneae_abdA.m8: alignment of arachnid abdA sequences against the draft genome

- plit.m8: MMseqs2 alignment results for the putative Hox sequences against the draft genome.

- r2_g3735-Alignment-HitTable.csv: NCBI BLAST results (nr) for gene r2_g3735


## 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.gff3: protein-coding gene models from all rounds of annotation

- 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)