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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>
Fig. 4 in Integrative redescription of Hypsibius pallidoides Pilato et al., 2011 (Eutardigrada: Hypsibioidea) with the erection of a new genus and discussion on the phylogeny of Hypsibiidae
Fig. 4. Hypsibius pallidoides Pilato, Kiosya, Lisi, Inshina & Biserov, 2011. A. Lateral view of the head region, white arrowhead indicates the anterior porous area, black arrowhead indicates the elliptical sensory organ, SEM. B. Enlarged view of the lateral surface of the head, white arrowhead indicates the anterior porous area, white arrow indicates the muscle attachment zone, SEM. C. Mouth opening with peribuccal lobes, SEM. D. Mouth opening with anterior ring of teeth, SEM. E. Dorsal sculpture of the juvenile, SEM. F. Bucco-pharyngeal apparatus (SPbU 251(82)), PhC. G. Dorsal view of the buccal cavity, black arrowhead indicates the circumoral elliptical structures (SPbU 251(82)), PhC. H. Ventral view of the buccal cavity, black arrowhead indicates the circumoral elliptical structures (SPbU 251(82)), PhC. Scale bars: A, F–H = 5 µm; B–C = 2 µm; D = 1 µm; E = 10 µm.
Fig. 7. A–G in Integrative redescription of Hypsibius pallidoides Pilato et al., 2011 (Eutardigrada: Hypsibioidea) with the erection of a new genus and discussion on the phylogeny of Hypsibiidae
Fig. 7. A–G. Hypsibius pallidoides Pilato, Kiosya, Lisi, Inshina & Biserov, 2011 eggs. A–D, specimen KNU Чер-9 II. A. Type series specimen mounted during the egg laying process, PhC. B. Type series egg shell, PhC. C. Type series egg shell, DIC. D. Type series egg shell structure with numerous internal pillars visible, DIC. E. Austrian population egg shell (SPbU 251(3)), PhC. F. Karelian population egg shell (SPbU 113(2)), PhC. G. Pushkin population egg shell (SPbU 235(28)), PhC. – H. Pilatobius recamieri (Richters, 1911), egg shell (SPbU 203(7)), PhC. Scale bars: A = 50 µm; B–H = 5 µm.
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>
FIGURES 15–20 in Redescription of Hypsibius microps Thulin, 1928 and H. pallidus Thulin, 1911 (Eutardigrada: Hypsibiidae) based on the type material from the Thulin collection
FIGURES 15–20. The type material of Hypsibius microps and Hypsibius pallidus from the Thulin collection: 15–17, H. microps (15, buccal apparatus (holotype); 16, claws III (holotype); 17, claws IV (holotype)); 18–20, H. pallidus (18, buccal apparatus (paratype); 19, claws III (holotype); 20, claws IV (paratype)). (scale on 18 same as on 15, and on 17, 19-20 same as on 16)
FIGURES 1–6 in Redescription of Hypsibius microps Thulin, 1928 and H. pallidus Thulin, 1911 (Eutardigrada: Hypsibiidae) based on the type material from the Thulin collection
FIGURES 1–6. The type material of Hypsibius microps and Hypsibius pallidus from the Thulin collection: 1–3, H. microps; 4–6, H. pallidus.
FIGURES 7–12 in Redescription of Hypsibius microps Thulin, 1928 and H. pallidus Thulin, 1911 (Eutardigrada: Hypsibiidae) based on the type material from the Thulin collection
FIGURES 7–12. Thulin's original drawings of H. microps and H. pallidus: 7–9, H. microps (7, buccal apparatus; 8, external claw III; 9, claws IV); 10–12, H. pallidus (10, buccal apparatus; 11, external claw III; 12, claws IV). (7–11 from Thulin 1928, 12 from Thulin 1911, not scaled)
FIGURES 13–14 in Redescription of Hypsibius microps Thulin, 1928 and H. pallidus Thulin, 1911 (Eutardigrada: Hypsibiidae) based on the type material from the Thulin collection
FIGURES 13–14. The type material of Hypsibius microps and Hypsibius pallidus from the Thulin collection: 13, H. microps, habitus (holotype); 14, H. pallidus, habitus (paratype). (scale on 14 same as on 13)
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.
FIGURE 4 in Hypsibius vaskelae, a new species of Tardigrada (Eutardigrada, Hypsibiidae) from Russia
FIGURE 4. Hypsibius pachyunguis (holotype). A—bucco-pharyngeal apparatus focused on the microplacoids (black arrow), B—bucco-pharyngeal apparatus focused on the second macroplacoid (black arrow points to the caudal constriction), C—claws of the second pair of legs, D—claws of the fourth pair of legs (black arrow points to the cuticular bar between the claw bases. A–D—phase contrast.
FIGURE 3. A–C in Hypsibius vaskelae, a new species of Tardigrada (Eutardigrada, Hypsibiidae) from Russia
FIGURE 3. A–C, Hypsibius marcelli: A—dorsal cuticular sculpture, B—legs I–II, C—legs IV. D; Hypsibius septulatus: claws of the third pair of legs; E, F, Hypsibius multituberculatus: E—dorsal cuticular sculpture, F—legs I–II; G–I, Hypsibius pradellii (holotype): G—dorsal cuticular sculpture, H—legs II–III, I—legs IV; J–N, Hypsibius scaber (J, K, M, N—holotype; Lparatype): J—dorsal cuticular sculpture, K—ventral cuticular sculpture, L—claws of the third pair of legs, M—claws of the fourth pair of legs, N—bucco-pharyngeal apparatus (black arrow points to the septula). A–N—phase contrast.
FIGURE 1 in Hypsibius vaskelae, a new species of Tardigrada (Eutardigrada, Hypsibiidae) from Russia
FIGURE 1. Hypsibius vaskelae sp. nov. A—habitus, B—dorsal sculpture in the caudal region of the body of the holotype, Cdorsal sculpture in the caudal region of the body of the paratype 1, D, E—dorsal sculpture in the caudal region of the body of the paratype 2. A, E—phase contrast; B–D—differential interference contrast.
FIGURE 2 in Hypsibius vaskelae, a new species of Tardigrada (Eutardigrada, Hypsibiidae) from Russia
FIGURE 2. Hypsibius vaskelae sp. nov. A—bucco-pharyngeal apparatus (focused on the macroplacoids), B—buccopharyngeal apparatus (focused on the dorsal buccal armature), C—claws of the second pair of legs (black arrow points to the cuticular bar between the claw bases, black arrowhead points to the cuticular bar near the base of the inner claw), D—claws of the fourth pair of legs (black arrow points to the cuticular bar between the claw bases, black arrowhead points to the cuticular bar near the base of the inner claw, white arrowheads points to the lunules), E—claws of the fourth pair of legs (black arrows points to the cuticular bars between the claw bases, F—drawing of the claws of the third pair of legs, G—drawing of the claws of the fourth pair of legs. (A–C, E–G—holotype, D—paratype 1). A–E—phase contrast.
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.
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