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The genome of the tardigrade Hypsibius dujardini
<p>These data files accompany the bioRxiv preprint "The genome of the tardigrade Hypsibius dujardini"</p> <p>Edinburgh genome assembly and annotation<br /> ========================================</p> <p>1. nHd.2.3.abv500.fna.gz - Edinburgh (EDI) genome assembly version 2.3. Reads were assembled as single-end with CLC to calculate the insert size distributions of the libraries and check for contaminants. Insert size distributions are calculated by mapping the reads back to the assembly with CLC. The MP library insert distribution wasn't normally distributed. The single-end assembly is checked for contamination using the blobtools software package which creates a TAGC plot. Inspection of the TAGC plot revealed multiple contaminations with distinct coverage and GC content that did not have a reference genome in public databases. The PE reads were normalised with one-pass khmer and were assembled with Velvet using a k-mer size of 55. Contaminants in the Velvet assembly were identified based on the coverage and GC of the scaffolds. The non-normalised reads were mapped to the assembly using CLC and reads were removed if either pair mapped to a contig identified as contaminant. The process was repeated two more times since newly assembled contaminants could be identified. Gaps were filled in the final assembly using GapFiller. Finally the MP library was used to scaffold the gap-filled assembly with SSPACE, accepting only the information from reads mapping 2 kb from the ends of the scaffolds. The final assembly spans 140 megabases (Mb) with median coverage of 86X.</p> <p>2. nHd.2.3.1.aug.gff.gz - Gene model GFF file as predicted by Augustus for nHd.2.3 genome assembly. This is Augustus run as a second pass annotation (using transcriptome assembly as evidence) after a first pass Maker (see below)</p> <p>3. nHd.2.3.1.aug.proteins.fasta.gz - Protein fasta file generated by Augustus for nHd.2.3 genome assembly.</p> <p>4. nHd.2.3.1.aug.transcripts.fasta.gz - Transcript CDS fasta file generated by Augustus for nHd.2.3 genome assembly.</p> <p><br /> Edinburgh genome assembly and annotation - intermediate files<br /> =============================================================</p> <p>1. nHd.1.0.contigs.cov.fna.gz - Preliminary assembly of all data, without any contamination screening</p> <p>2. maker1.gff3.gz - Gene model GFF file as generated by MAKER run as a first pass to generate enough genes to train genefinders more thoroughly</p> <p>3. all.maker.proteins.edit.fasta.gz - Protein fasta file generated by MAKER run as a first pass.</p> <p>4. all.maker.transcripts.edit.fasta.gz - Transcript CDS file generated by MAKER run as a first pass.</p> <p>Blob plots<br /> ==========</p> <p>1. nHd.2.3.nHd_lib350-cov.BlobDB.json.gz - A blobDB (a JSON file generated using the blobtools package) which contains mapping, assembly and taxonomic information for the Edinburgh assembly and our read data. http://drl.github.io/blobtools/</p> <p>2. nHd.1.0.BlobDB.json.gz - A blobDB (a JSON file generated using the blobtools package) which contains mapping, assembly and taxonomic information for the Edinburgh preliminary assembly nHd.1.0 and Edinburgh read data. http://drl.github.io/blobtools/</p> <p>3. unc.TG-cov.BlobDB.json.gz - A blobDB (a JSON file generated using the blobtools package) which contains mapping, assembly and taxonomic information for the UNC assembly and their read data. http://drl.github.io/blobtools/</p> <p>4. unc.nHd-cov.uniref.nt.BlobDB.json.gz - A blobDB (a JSON file generated using the blobtools package) which contains mapping, assembly and taxonomic information for the UNC assembly and the Edinburgh read data. http://drl.github.io/blobtools/</p> <p>5. tardi_RNASeq.vs.unc.bam.reads_cov.catcolour.txt.gz - Space delimited text file with classification of each UNC scaffold by avg coverage of each base by PolyA-selected RNAseq reads</p> <p>6. tardi_RNASeq.vs.nHd.2.3.bam.reads_cov.catcolour.txt.gz - Space delimited text file with classification of each Edinburgh scaffold by avg coverage of each base by PolyA-selected RNAseq reads</p> <p>H dujardini transcriptome data<br /> ==============================</p> <p>1. Trinity.fasta.c99.gz - Preliminary transcriptome assembly by Itai Yanai's lab. Please do not use in any publications without checking with yanailab.technion.ac.il first</p> <p> </p> <p>Abstract of bioRxiv paper at http://dx.doi.org/10.1101/033464</p> <p>====================================== <br /> The genome of the tardigrade Hypsibius dujardini <br /> ======================================</p> <p>Background: Tardigrades are meiofaunal ecdysozoans that may be key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through adoption of a cryptobiotic state. A recent high profile paper suggested that the genome of a model tardigrade, Hypsibius dujardini, has been shaped by unprecedented levels of horizontal gene transfer (HGT) encompassing 17% of protein coding genes, and speculated that this was likely formative in the evolution of stress resistance. We tested these findings using an independently sequenced and assembled genome of H. dujardini, derived from the same original culture isolate. </p> <p>Results: Whole-organism sampling of meiofaunal species will perforce include gut and surface microbiotal contamination, and our raw data contained bacterial and algal sequences. Careful filtering generated a cleaned H. dujardini genome assembly, validated and annotated with GSSs, ESTs and RNA-Seq data, with superior assembly metrics compared to the published, HGT-rich assembly. A small amount of additional microbial contamination likely remains in our 135 Mb assembly. Our assembly length fits well with multiple empirical measurements of H. dujardini genome size, and is 120 Mb shorter than the HGT-rich version. Among 23,021 protein coding gene predictions we found 216 genes (0.9%) with similarity to prokaryotes, 196 of which were expressed, suggestive of HGT. We also identified ~400 genes (<2%) that could be HGT from other non-metazoan eukaryotes. Cross-comparison of the assemblies, using raw read and RNA-Seq data, confirmed that the overwhelming majority of the putative HGT candidates in the previous genome were predicted from scaffolds at very low coverage and were not transcribed. Crucially much of the natural contamination in both projects was non-overlapping, confirming it as foreign to the shared target animal genome. </p> <p>Conclusions: We find no support for massive horizontal gene transfer into the genome of H. dujardini. Many of the bacterial sequences in the previously published genome were not present in our raw reads. In construction of our assembly we removed most, but still not all, contamination with approaches derived from metagenomics, which we show are very appropriate for meiofaunal species. We conclude that HGT into H. dujardini accounts for 1-2% of genes and that the proposal that 17% of tardigrade genes originate from HGT events is an artefact of undetected contamination.</p>
Unearthed from old soils: New records of Antarctic tardigrades, nematodes, and rotifers in the Prince-Charles Mountains
<p>Supplementary display items genarted by running the code associated with the pre-print "Unearthed from old soils: New records of Antarctic tardigrades, nematodes, and rotifers in the Prince-Charles Mountains". Sequence records will be availble via an online resource upon submission.</p>
Fig. 19 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 19. Tenuibiotus zandrae sp. nov. Egg chorion morphology seen in SEM. A. Entire egg. B. Magnification of the egg surface. C–F. Details of the egg processes and surface between them. Filled flat arrowheads indicate thickenings/striae on the surface between processes and filled indented arrowheads indicate small tubercles on the process walls. Scale bars in μm.
Fig. 18 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 18. Tenuibiotus zandrae sp. nov. Egg chorion morphology seen in PCM. A. Midsection under 400× magnification. B. Surface under 400× magnification. C–D. Surface between processes under 1000× magnification. E–H. Midsections of processes of four different eggs under 1000× magnification. Filled flat arrowheads indicate thickenings/striae which are visible as dark dots and lines on the surface between processes. Scale bars in μm.
Fig. 14 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 14. Tenuibiotus zandrae sp. nov. Claws (paratypes). A–B. Claws II and IV seen in PCM, respectively. C–D. Claws I and IV seen in SEM, respectively. Filled indented arrowhead indicates horseshoe structure connecting the anterior and the posterior claw. Scale bars in μm.
Fig. 11 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 11. Tenuibiotus zandrae sp. nov. Body granulation seen in PCM (paratypes). A–B. Uniformly distributed granulation on the dorso-cephalic and dorso-caudal part of the body. C–D. Uniformly distributed granulation on the dorso-cephalic and dorso-caudal part of the body with small, random patches of lacking granulation. E–F. Uniformly distributed granulation on the ventral side of the body without and with small random patches lacking granulation, respectively. A–B, E and C–D, F are from two different paratypes. Scale bars in μm.
Fig. 8 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 8. Macrobiotus engbergi sp. nov. Egg chorion morphology seen in SEM. A. Entire egg. B. Magnification of the egg surface. C–D. Details of the terminal discs. Scale bars in μm.
Fig. 4 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 4. Macrobiotus engbergi sp. nov. Claws (paratypes). A–B. Claws III and IV seen in PCM, respectively. C–D. Claws III and IV seen in SEM, respectively. Filled flat arrowheads indicate double muscles attachments under the claws, empty flat arrowhead indicates inverted horseshoe structure under the external and the internal claw, whereas filled indented arrowhead indicates horseshoe structure connecting the anterior and the posterior claw. Scale bars in μm.
Fig. 5 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 5. Macrobiotus engbergi sp. nov. Buccal apparatus and the oral cavity armature seen in PCM (holotype, IZiBB, slide GL.052.22). A. Dorso-ventral projection of the entire buccal apparatus. B–C. Oral cavity armature visible in dorsal (B) and ventral (C) view, respectively. D–E. Placoid morphology visible in dorsal (D) and ventral (E) view, respectively. Filled flat arrowheads indicate the second band of teeth in the oral cavity, empty flat arrowheads indicate the third band of teeth in the oral cavity, empty indented arrowheads indicate central constrictions in the first macroplacoids and subterminal constriction in the second macroplacoids. Scale bars in μm.
Fig. 12 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 12. Tenuibiotus zandrae sp. nov. Patches of dense granulation on legs seen in PCM (paratypes). A. External granulation on leg III (patch of dense granulation encircled). B. Internal granulation on leg III. C. Granulation on leg IV. Scale bars in μm.
Fig. 21 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 21. Tenuibiotus voronkovi (Tumanov, 2007) Egg chorion morphology seen in PCM. A. Midsection under 400× magnification. B. Surface between processes under 1000× magnification. C–J. Details of egg processes under 1000× magnification. Filled flat arrowhead indicates thickenings/striae/sculpture which are visible as dark dots on the surface between processes and indented empty arrowheads indicate broken apices of the egg processes. Scale bars in μm.
Fig. 20 in Integrative taxonomy identifies two new tardigrade species (Eutardigrada: Macrobiotidae) from Greenland
Fig. 20. Tenuibiotus voronkovi (Tumanov, 2007). Body granulation seen in PCM. A. Uniformly distributed granulation of uniform size on the dorso-medial part of the body (cephalic region, paratype). B. Patch of dorso-lateral granulation composed of granules of different size (holotype). Scale bars in μm.
Fig. 5 in A new tardigrade species of the genus Neostygarctus Grimaldi de Zio et al., 1982 (Tardigrada, Arthrotardigrada) from the Great Meteor Seamount, Northeast Atlantic
Fig. 5. Neostygarctus grossmeteori sp. nov. Paratype, ♀ (SMF 52), details. A. Lateral body processes, ventral view. B–D. Legs I (left and right) and IV. E. Genital area. Scale bars: A = 50 μm; B–E = 20 μm.
Fig. 2 in A new tardigrade species of the genus Neostygarctus Grimaldi de Zio et al., 1982 (Tardigrada, Arthrotardigrada) from the Great Meteor Seamount, Northeast Atlantic
Fig. 2. Neostygarctus grossmeteori sp. nov., entire. A. Holotype, ♀ (SMF 51), dorsal view. B. Paratype, Ƌ (SMF 58), ventral view. Scale bar = 100 μm.
Fig. 1 in A new tardigrade species of the genus Neostygarctus Grimaldi de Zio et al., 1982 (Tardigrada, Arthrotardigrada) from the Great Meteor Seamount, Northeast Atlantic
Fig. 1. Type locality and milieu of Neosstygarctus grossmeteori sp. nov. A. Position of the Great Meteor Seamount in the Atlantic Ocean. B. Bioclastic sediment consisting mainly of calcareous foraminiferan and pteropod shells (fine fraction of sediment washed off). Scale bar = 2 mm.
Fig. 4 in A new tardigrade species of the genus Neostygarctus Grimaldi de Zio et al., 1982 (Tardigrada, Arthrotardigrada) from the Great Meteor Seamount, Northeast Atlantic
Fig. 4. Neostygarctus grossmeteori sp. nov., optical photopictures. A. Paratype, ♀ (SMF 54), entire body, dorsal view. B. Holotype, ♀ (SMF 51), entire body, ventral view. C–E. Paratype of obscure gender (SMF 59). C–D. Areas of dorsal surface of body with spines. E. Lateral body projections. F. Holotype, ♀ (SMF 51), posterior body with female gonopore and anus. Scale bars: A–B = 50 μm; C–F = 20 μm.
Fig. 3 in A new tardigrade species of the genus Neostygarctus Grimaldi de Zio et al., 1982 (Tardigrada, Arthrotardigrada) from the Great Meteor Seamount, Northeast Atlantic
Fig. 3. Neostygarctus grossmeteori sp. nov., heads. A. Holotype, ♀ (SMF 51), dorsal view. B. Paratype, ♀ (SMF 52), ventral view. Scale bar = 50 μm.
Fig. 6 in A new tardigrade species of the genus Neostygarctus Grimaldi de Zio et al., 1982 (Tardigrada, Arthrotardigrada) from the Great Meteor Seamount, Northeast Atlantic
Fig. 6. Neostygarctus grossmeteori sp. nov., details, SEM. A. Female, entire body, ventral view. B. Right secondary clava and outer cirrus on the head, ventral view. C. Ventral conical spikes on the basal part of the lateral body process. D. Right lateral body processes. E. Lateral fan of spines with membrane on the posteriormost body segment. F. Toes with claws of the leg IV ventrally, dorsal tendon detached in some toes. G. Inner and outer claws, dorsal view. H. Accordion-like joint of the cirrus E. Scale bars: A = 30 μm; B, D, F = 10 μm; C, E, G–H = 3 μm.
Figs 24–29 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 24–29. Macrobiotus polypiformis sp. nov. 24. Chorion. 25. Long, hair-like flexible filaments on terminal discs. 26. Egg processes with faint annular undulations. 27. Surface between egg processes with reticular design. 28. Terminal discs with small, randomly arranged granules. 29. Small granules on filaments. All in SEM. Scale bars in μm.
Figs 20–23 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 20–23. Macrobiotus polypiformis sp. nov. 20. Chorion. 21. Long, hair-like flexible filaments on terminal discs. 22. Egg processes and the surface between egg processes with reticular design. 23. Egg processes with filaments. All in PCM. Scale bars in μm.
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