Find research datasets worth reusing

Fig. 11 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 11. Nymphon dorlis sp. nov., holotype, ♂, MNHN-IU-2016-879. A. Body, dorsal view. B. Body, lateral view (same scale as A). C. Palp. D. Oviger. E. Pointed teeth of oviger. F. Chela. G. Third leg. H. Tarsus and propodus of third leg.

Fig. 15 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 15. Nymphon timons sp. nov., holotype, ♀, MNHN-IU-2016-844. A. Body, dorsal view. B. Body, lateral view (same scale as A). C. Fourth leg. D. Tarsus and propodus of fourth leg. E. Chela. F. Palp. G. Oviger. H. Oviger strigilis. I. Compound denticle and terminal claw of strigilis.

Fig. 8 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 8. Ascorhynchus sp. 5, juvenile, MNHN-IU-2016-1039. A. Body, dorsal view. B. Body, lateral view (same scale as A). C. Palp. D. First leg. E. Tarsus and propodus of first leg. F. Chela.

Fig. 9 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 9. Comparison between Eurycyde kaiouti sp. nov. (A–J) and E. raphiaster Loman, 1912 (K). A–J. Holotype, ♂, MNHN-IU-2016-1129. K. ♂, MNHN-IU-2016-818. A. Body, dorsal view. B. Body, lateral view (same scale as A). C. Oviger. D. Oviger strigilis. E. Pointed teeth of oviger strigilis. F. Third leg. G. Tarsus and propodus of third leg. H. Chelifore. I. Chela bud. J. Palp. K. Body, dorsal view (same scale as A).

Fig. 17 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 17. Endeis aff. meridionalis (Böhm, 1879), ♂, MNHN-IU-2016-1043. A. Body, dorsal view. B. Body, lateral view (same scale as A). C. Oviger. D. Last two oviger articles. E. Third leg.

Fig. 5 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 5. Comparison between Tanystylum boucheti sp. nov. (A–H) and T. hummelincki Stock, 1954 (I– J). A–H. Holotype, ♂, MNHN-IU-2016-1074. I–J. ♂, MNHN-IU-2016-1063. A. Body, dorsal view. B. Body, lateral view (same scale as A). C. Palp. D. Third leg. E. Cement gland tube. F. Tarsus and propodus of third leg. G. Oviger. H. Oviger strigilis. I. Body, dorsal view. J. Body, lateral view. I and J same scale as A.

Fig. 1 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 1. Madibenthos sampling stations with occurrences of sea spiders in Martinique. Bathymetric range is shown by grey isolines each 20 m (0–100 m depth) and each 500 m (deeper than 500 m). The 100 m isobath (above which most samplings were performed) is marked by a black isoline. Sampling stations are indicated as black circles. See Sabroux et al. (2019b) for alternative representation.

Fig. 14 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 14. Nymphon martinicum sp. nov. A–K. Holotype, ♂, MNHN-IU-2016-889. L–M. Paratype, ♀, MNHN-IU-2016-1033. A. Body, dorsal view. B. Body, lateral view (same scale as A). C. Ocular tubercle, frontal view. D. Palp. E. Chelifore. F. Leg. G. Tarsus and propodus. H. Close-up of ventral surface of propodal claws. I. Oviger. J. Oviger strigilis. K. Pointed teeth of oviger strigilis. L. Chela (same scale as E). M. Ocular tubercle, frontal view (same scale as C).

Posterior regeneration in the sea spider Pycnogonum litorale (Arthropoda, Pycnogonida)

<p><em>Pycnogonum litorale</em>; micro-computed X-ray tomography raw data (3D tiff file format) of specimens subjected to varying degrees of posterior amputation and individually monitored following the surgery.</p>

opencc-by-4.0Nov 2024View details →

Supplemental data for "The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with reduced posterior tagma"

<div># List of files on Zenodo</div> <p> </p> <div>Data accompanying the manuscript have been uploaded on Zenodo (10.5281/zenodo.14185694). Here we</div> <div>present a brief description of each file and put them in meaningful groups.</div> <p> </p> <div>## referenced supplement</div> <p> </p> <div>(Cited) supplementary material from the manuscript. For more information, please refer to the figure/table legends and the supplementary file descriptions.</div> <p> </p> <div> <div>- add-file-01.pdf</div> <div>- add-file-02-table1-data_overview.tsv</div> <div>- add-file-03-table2-genome_progress.tsv</div> <div>- add-file-04-table3-Pycnognonum_microRNAs.tsv</div> <div>- add-file-05-table4-named_genes.tsv</div> <div>- add-file-06-table5-abdA.tsv</div> <div>- add-file-07-hox_tree.pdf</div> <div>- add-file-08-table6-r2_g3735-Alignment-HitTable.tsv</div> <div>- add-file-09-hro_tree.pdf</div> <div>- add-file-10-irx_tree.pdf</div> <div>- add-file-11-sine_tree.pdf</div> <div>- add-file-12-nk_tree.pdf</div> <div>- add-file-13-dbx.png</div> <div>- add-file-14-alignment.pdf</div> <div>- add-file-15-Plit_COI-alignment_distances.pdf</div> <div>- add-file-16-table7-isoseq.tsv</div> <div>- add-file-17-table8-chelicerate_repeat_content.tsv</div> <div>- add-file-18-table9-arthropod_genomes.tsv</div> <div>- add-file-19-table10-arthropod_repeat_content.tsv</div> <div>- add-file-20-table11-chelicerate_genomes.tsv</div> <div>- add-file-21-gene_analysis.zip</div> <div>- add-file-22-table12-self_synteny.tsv</div> </div> <p> </p> <div>## figures</div> <p> </p> <div>- figs.zip: archive of raw and processed figures for the manuscript in full resolution</div> <p> </p> <div>## analysis</div> <p> </p> <div>### genomic context</div> <p> </p> <div>The broader arthropod/chelicerate context for the _P. litorale_ genome assembly.</div> <p> </p> <div>- araneae.tsv: repeat makeup of published chelicerate assemblies</div> <div>- arthropoda.tsv: genome assembly statistics for arthropod genomes. From NCBI Genomes.</div> <div>- modern_taxids.txt: list of taxonomic IDs for species; made to be submitted to NCBI Taxonomy.</div> <div>- tax_report.txt: the full taxonomic report for each query species. Contains tax IDs for the entire lineage.</div> <div>- total_repeats.tsv: total repeat content of published chelicerate genomes.</div> <p> </p> <div>### Homeobox genes</div> <p> </p> <div>Files concerning the Homeobox gene cluster analysis. Each folder (hro, irx, nkx, sine) contains the</div> <div>candidate sequences from Aase-Remedios et al., the P. litorale sequences that matched, the multiple</div> <div>sequence alignment, the trimmed alignment, and the tree files.</div> <p> </p> <div>Additionally, the hox/ folder contains the analysis done for the AbdA gene, with searches performed</div> <div>against the de-novo assembled transcriptomes (.m8 files).</div> <p> </p> <div>Finally, the r2_g3735/ folder contains the analysis of the r2_3735 gene model, which is found in the</div> <div>Hox cluster area on the P. litorale genome. Sequence searches against NCBI nr and the developmental</div> <div>transcriptomes show that the gene has putative homologs in other taxa and is expressed throughout</div> <div>development.</div> <p> </p> <div>## processed (intermediate) data</div> <p> </p> <div>### 00-kmer-jellyfish.zip</div> <p> </p> <div>k-mer spectra analysis with GenomeScope and GenomeScope2.0</div> <p> </p> <div>### 00-seq-qc.zip</div> <p> </p> <div>quality control output for raw sequencing data (e.g. FastQC output)</div> <p> </p> <div>### 01-assembly</div> <p> </p> <div>- assembly_graph.gfa: Flye output</div> <div>- assembly_graph.gv: Flye output</div> <div>- assembly_info.txt: Flye output</div> <div>- assembly.fasta: Flye output</div> <div>- backmap.hifi.sort.bam.cov-hist.pdf: coverage histogram of the back-mapped PacBio data</div> <div>- backmap.ont.sort.bam.cov-hist.pdf: coverage histogram of the back-mapped ONT data</div> <div>- BUSCO.arthropoda_odb10.txt: BUSCO completeness report (arthropoda_odb10)</div> <div>- BUSCO.metazoa_odb10.txt: BUSCO completeness report (metazoa_odb10)</div> <div>- flye.log: Flye assembler log</div> <div>- quast_report.pdf: assembly QC</div> <p> </p> <div>### 02-scaffold</div> <p> </p> <div>`yahs` output files:</div> <p> </p> <div>- asm_hic.sorted.bam</div> <div>- flye-yahs.fa</div> <div>- yahs.out_scaffolds_final.agp</div> <div>- yahs.out_scaffolds_final.fa.hic</div> <div>- yahs.out_scaffolds_final.fa.assembly</div> <p> </p> <div>Juicebox (manual curating) results:</div> <p> </p> <div>- yahs.out_scaffolds_final.fa.review.assembly</div> <div>- 02-flye-yahs-juicebox.fa</div> <p> </p> <div>GAP `sort_scaffolds` pipeline outputs</div> <p> </p> <div>- 03-flye-yahs-juicebox-merge.fasta</div> <div>- plit_q_0_50000_0.5FracBest_unseen_scaffolds.txt</div> <div>- plit_q_0_50000_0.5FracBest_insertion_stats.tsv</div> <div>- plit_q_0_50000_0.5FracBest_appended_scaffolds.tsv</div> <div>- plit_q_0_50000_0.5FracBest_inserted_scaffolds.tsv</div> <p> </p> <div>### 03-contamination</div> <p> </p> <div>Refer to the [contamination analysis](https://github.com/galicae/plit-genome/blob/main/04-contam/README.md) for details.</div> <p> </p> <div>Decontaminating the draft genome from non-metazoan scaffolds:</div> <p> </p> <div>- plit_q_0_50000_0.5FracBest_output_filtered.fasta: input draft genome</div> <div>- contam_tax.m8: Alignment results of UniRef90 against draft genome (MMseqs2)</div> <div>- scaffolds_taxonomic_distribution.tsv: summary of contam_tax.m8; number of genes from each taxonomic level per scaffold.</div> <div>- scaffolds_taxonomic_distribution_collapsed_vir.tsv: scaffolds with predominantly viral hits</div> <div>- scaffolds_taxonomic_distribution_suspect.tsv: scaffolds whose genes are <90% metazoan</div> <p> </p> <div>Checking for widespread _Metridium_ contamination:</div> <p> </p> <div>- primary_mq30.txt: list of high-quality mapping reads (presumptive "metridial")</div> <div>- metridium_scaffolds.txt_summary: no. of presumptive _Metridium_ reads per draft scaffold</div> <div>- metridium_scaffolds.txt: filtered SAM file with all high-quality "_Metridium_" hits on draft scaffolds</div> <div>- metridium_contigs.sam_summary: no. of presumptive _Metridium_ reads per Flye contig</div> <p> </p> <div>### 04-annotation</div> <p> </p> <div>Repeat analysis with RepeatModeler/RepeatMasker:</div> <p> </p> <div>- draft.fasta.tbl: output of RepeatModeler in tabular form</div> <div>- pb.sam.flagstats: summary of mapping the repeat families to the PacBio data.</div> <div>- pycno-families.fa: output of RepeatModeler - the sequences of the _P. litorale_ repeat families</div> <div>- draft.fasta.out.gff: output of RepeatModeler - repeat locations on the draft genome</div> <p> </p> <div>Protein coding gene annotation:</div> <p> </p> <div>- annot-01-isoseq.gff: GFF file with the gene models proposed using Iso-seq isoforms</div> <div>- annot-01-braker.gff: GFF file with the gene models proposed from round 1 of BRAKER3 using developmental transcriptomes</div> <div>- 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</div> <div>- annot-03-denovo.gff3: GFF file with the gene models proposed from the de novo transcriptomes</div> <div>- deep_denovo_assemblies.zip: the de-novo assembled transcriptomes from the deeply sequenced developmental time points. Also available on ENA.</div> <p> </p> <div>tRNAscan output</div> <p> </p> <div>- trnascan.bed</div> <div>- trnascan.out</div> <div>- trnascan.fasta</div> <div>- trnascan.stats</div> <p> </p> <div>MirMachine output</div> <p> </p> <div>- Pli_september.PRE.gff: MirMachine output with permissive threshold</div> <div>- Pli_september.PRE-1.gff: MirMachine output with strict threshold</div> <div>- Pli_september.PRE.fasta: predicted miRNA sequences</div> <p> </p> <div>## Results</div> <p> </p> <div>- draft_softmasked.fasta: draft genome with repetitive regions softmasked</div> <div>- draft.fasta: draft genome fasta</div> <div>- hox.gff3: the position of the Hox genes in GFF3 form.</div> <div>- merged_sorted_named_dedup_flagged.gff3: protein-coding gene models from all rounds of annotation after deduplication</div> <div>- transcripts.fa: TransDecoder-extracted putative transcripts</div> <div>- transcripts.fa.transdecoder.pep: TransDecoder predicted peptides</div> <div>- out.emapper.annotations: EggNOG-mapper functional annotation for the predicted peptides</div> <div>- out.emapper.best.annotations: filtered EggNOG-mapper annotation; best hit per gene kept</div> <div>- miRNA.fasta: FASTA sequences of predicted miRNAs</div> <div>- miRNA.lenient.gff: GFF of miRNA positions (permissive MirMachine cutoff)</div> <div>- miRNA.strict.gff: GFF of miRNA positions (strict MirMachine cutoff)</div>

opencc-by-4.0Oct 2018View details →

Figure 1 in Checklist of sea spiders (Arthropoda: Pycnogonida) from the Persian Gulf and the Gulf of Oman with new record of Endeis biseriata (Böhm, 1879) for the region

Figure 1. Sampled area and location of Chabahar Bay in the Gulf of Oman.

Fig. 16 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 16. Nymphon timons sp. nov., paratype, ♂, MNHN-IU-2021-6623. Oviger.

Fig. 13 in Sea spiders (Arthropoda: Pycnogonida) collected during the Madibenthos Expedition from Martinique shallow waters

Fig. 13. Nymphon ludovici sp. nov., paratype, ♀, MNHN-IU-2017-219. Chelifore.

opencc-by-4.0Feb 2023View details →

Observation of mating behavior in giant sea spiders (Pycnogonida: Colossendeidae)

<p>Close-up view of the mating behavior in <em>Colossendeis</em> sp. captured during E/V <em>Nautilus</em> expedition NA137 on high-definition ROV video at a depth of ~1700 m on an unnamed seamount located ~70 km north of Kingman Reef (Dive H1911, 7.06750°N, 162.53226°W, 27 March 2022), within the Pacific Remote Islands Marine National Monument. The expedition was supported by NOAA Ocean Exploration through the Ocean Exploration Cooperative Institute, and executed under permit 12543-22002 authorized by the U.S. Fish and Wildlife Service. Video courtesy of Ocean Exploration Trust.</p>

opennotspecifiedJun 2020View details →

FIGURE 1 in Recent collections of sea spiders (Arthropoda: Pycnogonida) from China seas, with some new records and a checklist of the area

FIGURE 1. Sampled location of this study. ▲—Ascorhynchus ramipes (Böhm, 1879); ◆—Paranymphon spinosum Caullery 1896; ╋—Propallene sp.; ●—Ammothea hilgendorfi (Böhm, 1879); █—Anoplodactylus eroticus Stock, 1968;▼—Propallene species indet.

opennotspecifiedJun 2020View details →

FIGURE 3. Anoplodactylus eroticus Stock, 1968 in Recent collections of sea spiders (Arthropoda: Pycnogonida) from China seas, with some new records and a checklist of the area

FIGURE 3. Anoplodactylus eroticus Stock, 1968 (P18–B0911SL6–01) male, a. trunk, dorsal view; b. trunk, lateral view; c. trunk, ventral view; d. ventrally spurs on the second coxae of leg 2 and 3; e. tarsus, propodus and claw of leg 2, arrows indicating the sole spines; f. tarsus, propodus and claw of leg 3, arrows indicating the sole spines. Scale bars a, b=1 mm, c, d =0.5 mm, e, f=0.2 mm.

FIGURE 2. Crocydocinus saravananei n in Description of a new species of deep-sea spider crab from the genus Crocydocinus Lee, Richer de Forges & Ng, 2019, from the south-eastern Arabian Sea (Crustacea Decapoda: Majoidea: Epialtidae)

FIGURE 2. Crocydocinus saravananei n. sp., holotype, male (30.8 × 26.7 mm) (IO/SS/BRC/00180), Arabian Sea. A, overall dorsal view of carapace; B, lateral view of carapace, C, overall ventral view; D, dorsal view of anterior portion of carapace; E, ventral frontal view; F, right cheliped; G, ventral view of right cheliped; H, P2 dactylus; I, P3 dactylus, J, P4 dactylus; K, male pleon.

FIGURE 3. Crocydocinus saravananei n in Description of a new species of deep-sea spider crab from the genus Crocydocinus Lee, Richer de Forges & Ng, 2019, from the south-eastern Arabian Sea (Crustacea Decapoda: Majoidea: Epialtidae)

FIGURE 3. Crocydocinus saravananei n. sp., holotype male (30.8 × 26.7 mm) (IO/SS/BRC/00180), Arabian Sea, left G1 and G2. A, ventral view; B, ventral view of distal portion; C, dorsal view; D, dorsal view of distal portion; E, ventral view of G2; F, dorsal view of G2.

FIGURE 6. Pigrogromitus timsanus Calman, 1927 in A new species of Achelia (Pycnogonida: Ammotheidae) and first records of intertidal sea spiders found on Zoanthus (Cnidaria: Zoantharia) from Karachi Pakistan

FIGURE 6. Pigrogromitus timsanus Calman, 1927, male: (A) dorsal view; (B) lateral view; (C) chelifore; (D) oviger; (E) 3rd leg; (F) claw of propodus. Scale bar: (A–B) 0.5mm; (C) 0.1 mm; (D) 0.25 mm; (E–F) 0.1 mm.

FIGURE 10 in A new species of Achelia (Pycnogonida: Ammotheidae) and first records of intertidal sea spiders found on Zoanthus (Cnidaria: Zoantharia) from Karachi Pakistan

FIGURE 10. Anoplodactylus aff. nanus Krapp, Kocak & Katagan, 2008, male: (A) dorsal view; (B) lateral view; (C) oviger; (D) 3rd leg; (E) claw of propodus. Scale bar: (A, B and D) 0.5 mm; (C) 0.2 mm; (E) 0.1 mm.