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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>
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini
<p><strong>No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini</strong></p> <p>These files accompany the peer-reviewed version of http://dx.doi.org/10.1101/033464</p> <p>A previous dataset https://zenodo.org/record/45162 accompanied the version of this manuscript at BioRxiv - biorxiv.org/content/early/2015/12/13/033464</p> <p>This dataset includes all files from https://zenodo.org/record/45162 plus all the Supplemental files, and one additional file HGT_phylogenetic_files.tgz. All files are described in Hypsibius_dujardini_files_README.md</p> <p><strong>Abstract</strong></p> <p>Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper (Boothby TC <em>et al </em>(2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. <em>Proc Natl Acad Sci USA</em> 112:15976-15981) the authors concluded that the tardigrade <em>Hypsibius dujardini </em>had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT), and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of <em>H. dujardini</em>. As expected from whole-organism DNA sampling, our raw data contained reads from non-target genomes. Filtering using metagenomics approaches generated a draft <em>H. dujardini</em> genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria, and 0.2% strong candidates for fHGT from non-metazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby <em>et al.</em> genome derived from contaminants. We conclude that fHGT into <em>H. dujardini </em>accounts for at most 1-2% of genes and that the proposal that one sixth of tardigrade genes originate from functional HGT events is an artefact of undetected contamination.</p> <p> </p>
Figure 2 in Radiation tolerance and bystander effects in the eutardigrade species Hypsibius dujardini (Parachaela: Hypsibiidae)
Figure 2. Radiation and radiation-induced bystander effects on the eutardigrade species Hypsibius dujardini. Survivorship curves following direct (RAD) and indirect (BYST) exposure to 3 and 5 kGy gamma radiation.
Figure 1 in Radiation tolerance and bystander effects in the eutardigrade species Hypsibius dujardini (Parachaela: Hypsibiidae)
Figure 1. Experimental set-up for testing radiation tolerance and bystander effects in the eutardigrade species Hypsibius dujardini: control (CON; 0 kGy), irradiated [received 3 kGy (RAD3) and 5 kGy (RAD5) gamma radiation] and bystander [exposed to an individual irradiated at the 3 kGy (BYST3) or 5 kGy (BYST5) level] groups.
FIGURES 9–12 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURES 9–12. Hypsibius exemplaris sp. nov.: 9—adult habitus (ventrolateral view, PCM, holotype); 10—adult habitus (lateral view, SEM, paratype); 11 —bucco-pharyngeal apparatus, the arrowhead indicates large pharyngeal apophyses (PCM, paratype); 12—bucco-pharyngeal apparatus (SEM, paratype). All scale bars in µm.
FIGURES 25–29 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURES 25–29. Hypsibius cf. convergens (Urbanowicz, 1925) from Poland, seen in PCM: 25—habitus, ventral view; 26— bucco-pharyngeal apparatus; 27—claws I; 28—claws IV; Hypsibius pallidus Thulin, 1911 from Poland, seen in PCM: 29— claws IV. All scale bars in µm.
FIGURES 5–8 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURES 5–8. Hypsibius dujardini (Doyère, 1840), claws: 5—claws I (PCM, neoparatype); 6—claws IV, the arrowhead indicates the longitudinal bar at the posterior claw base, and the empty arrowhead indicates the pseudolunula at the anterior claw base (PCM, neoparatype); 7—claws II (SEM, neoparatype); 8—claws IV, the empty arrowhead indicates the pseudolunula at the anterior claw base (SEM, neoparatype). All scale bars in µm.
FIGURES 32–36 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURES 32–36. Ramazzottius cf. conifer comb. nov. (Mihelčič, 1938) from Scotland, seen in PCM: 32—habitus, ventral view; 33—claws I; 34—claws IV; 35—egg, note underdeveloped processes in the upper right part of the egg; 36—the other side of the same egg, note rows of connected processes characteristic for the species. All scale bars in µm.
FIGURES 1–4 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURES 1–4. Hypsibius dujardini (Doyère, 1840): 1—adult habitus (ventrolateral view, PCM, neotype); 2—ex ovo juvenile habitus (ventral view, PCM, neoparatype); 3—bucco-pharyngeal apparatus (dorso-ventral projection, the arrowhead indicates large pharyngeal apophyses, PCM, neoparatype); 4—bucco-pharyngeal apparatus (ventral view, SEM, neoparatype). All scale bars in µm.
FIGURES 17–24 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURES 17–24. Details of the bucco-pharyngeal apparatus of the Hypsibius type (in SEM): 17—peribuccal ring and the oral cavity armature of H. dujardini, the arrow indicates the row of conical teeth located on the ring fold; 18—oral cavity armature of H. exemplaris sp. nov., the arrow indicates the row of conical teeth located on the ring fold whereas the empty arrowhead indicates the porous area on the lateral wall of the cavity; 19—the buccal crown and the dorsal apophyses for insertion of stylet muscles (AISM) of H. exemplaris; 20—the buccal crown and both dorsal and ventral apophyses for insertion of stylet muscles (AISM) of H. exemplaris sp. nov. in lateral view; 21—furca of H. exemplaris sp. nov., external side; 22—furca of H. dujardini, internal side with the stylet support; 23—pharynx of H. dujardini, arrowheads point out evident macroplacoid constrictions; 24—pharynx of H. exemplaris sp. nov., arrowheads point out subtle macroplacoid constrictions. All scale bars in µm.
FIGURE 31 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURE 31. An ML COI-based phylogenetic tree of the subfamily Hypsibiinae with; Mesocrista spitzbergensis (Itaquasconinae) as an outgroup. ML bootstrap support values are presented below tree branches.
FIGURE 30. A in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURE 30. A Bayesian phylogenetic tree of the family Hypsibiidae based on 18S rRNA sequences, with two Macrobiotus spp. as an outgroup. Bayesian posterior probability values are given above tree branches whereas ML support values are below branches. The scale refers to the Bayesian tree.
FIGURES 13–16 in An integrative redescription of Hypsibius dujardini (Doyère, 1840), the nominal taxon for Hypsibioidea (Tardigrada: Eutardigrada)
FIGURES 13–16. Hypsibius exemplaris sp. nov., claws: 13—claws III (PCM, holotype); 14—claws IV, arrowhead points longitudinal bar at the posterior claw basis, and empty arrowhead indicates pseudolunula at the anterior claw basis (PCM, paratype); 15—claws III (SEM, paratype); 16—claws IV, arrowhead points longitudinal bar at the posterior claw basis, and empty arrowhead indicates pseudolunula at the anterior claw basis (SEM, paratype). All scale bars in µm.
FIGURE 1. A in Tardigrades of the Australian Antarctic: Hypsibius heardensis (Eutardigrada: Hypsibiidae: dujardini group) a new species from sub-Antarctic Heard Island
FIGURE 1. A, Antarctica and the subAntarctic islands in a polar projection, showing the position of Heard Island. B, Heard Island. Red Island, a promontory off Laurens Peninsula to the northwest indicated with an arrow.
FIGURE 3 in Tardigrades of the Australian Antarctic: Hypsibius heardensis (Eutardigrada: Hypsibiidae: dujardini group) a new species from sub-Antarctic Heard Island
FIGURE 3. Hypsibius heardensis sp. nov. A, dorsal view buccal apparatus. B, lateral view buccal apparatus. C, claws of legs III. D, claws of legs IV. Scale bars = 10 micrometers.
FIGURE 2 in Tardigrades of the Australian Antarctic: Hypsibius heardensis (Eutardigrada: Hypsibiidae: dujardini group) a new species from sub-Antarctic Heard Island
FIGURE 2. Hypsibius heardensis sp. nov. A, habitus (lateral view). B–C, buccal apparatus (B – dorsal view, C – lateral view). D, claws of legs III. E, claws of legs IV.
Data from: Tolerance to gamma radiation in the tardigrade Hypsibius dujardini from embryo to adult correlate inversely with cellular proliferation
Tardigrades are highly tolerant to desiccation and ionizing radiation but the mechanisms of this tolerance are not well understood. In this paper, we report studies on dose responses of adults and eggs of the tardigrade Hypsibius dujardini exposed to gamma radiation. In adults the LD50/48h for survival was estimated at ~ 4200 Gy, and doses higher than 100 Gy reduced both fertility and hatchability of laid eggs drastically. We also evaluated the effect of radiation (doses 50 Gy, 200 Gy, 500 Gy) on eggs in the early and late embryonic stage of development, and observed a reduced hatchability in the early stage, while no effect was found in the late stage of development. Survival of juveniles from irradiated eggs was highly affected by a 500 Gy dose, both in the early and the late stage. Juveniles hatched from eggs irradiated at 50 Gy and 200 Gy developed into adults and produced offspring, but their fertility was reduced compared to the controls. Finally we measured the effect of low temperature during irradiation at 4000 Gy and 4500 Gy on survival in adult tardigrades, and observed a slight delay in the expressed mortality when tardigrades were irradiated on ice. Since H. dujardini is a freshwater tardigrade with lower tolerance to desiccation compared to limno-terrestrial tardigrades, the high radiation tolerance in adults, similar to limno-terrestrial tardigrades, is unexpected and seems to challenge the idea that desiccation and radiation tolerance rely on the same molecular mechanisms. We suggest that the higher radiation tolerance in adults and late stage embryos of H. dujardini (and in other studied tardigrades) compared to early stage embryos may partly be due to limited mitotic activity, since tardigrades have a low degree of somatic cell division (eutely), and dividing cells are known to be more sensitive to radiation.
Data from: Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in Panarthropoda
<p>Screening of a deeply sequenced transcriptome using Illumina sequencing as well as the genome of the tardigrade <em>Hypsibius exemplaris </em>(referred to as <em>Hypsibius dujardini </em>in the published article) revealed a set of five opsin genes.To clarify the phylogenetic position of these genes and to elucidate the evolutionary history of opsins in Panarthropoda (Onychophora +Tardigrada+Arthropoda), we reconstructed the phylogeny of broadly sampled metazoan opsin genes using maximum likelihood and Bayesian inference methods in conjunction with carefully selected substitution models. According to our findings, the opsin repertoire of <em>H. exemplaris</em> comprises representatives of all three major bilaterian opsin clades, including one r-opsin, three c-opsins, and a Group 4 opsin (neuropsin/opsin-5). The identification of the tardigrade ortholog of neuropsin/opsin-5 is the first record of this opsin type in a protostome,but our screening of available metazoan genomes revealed that it is also present in other protostomes. Our opsin phylogeny further suggests that two r-opsins, including an "arthropsin", were present in the last common ancestor of Panarthropoda. Although both r-opsin lineages were retained in Onychophora and Arthropoda, the arthropsin was lost in Tardigrada. The single (most likely visual) r-opsin found in <em>H. exemplaris</em> supports the hypothesis of monochromatic vision in the panarthropod ancestor, whereas two duplications of the ancestral panarthropod c-opsin have led to three c-opsins in tardigrades. Although the early-branching nodes are unstable within the metazoans, our findings suggest that the last common ancestor of Bilateria possessed six opsins: Two r-opsins, one c-opsin, and three Group 4 opsins, one of which (Go opsin) was lost in the ecdysozoan lineage.</p>
Data from: Tolerance to gamma radiation in the tardigrade Hypsibius dujardini from embryo to adult correlate inversely with cellular proliferation
Open the record for dataset details and reuse information.
Data from: Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in Panarthropoda
Open the record for dataset details and reuse information.
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