Dataset Open Access

No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

Koutsovoulos, Georgios; Kumar, Sujai; Laetsch, Dominik R; Stevens, Lewis; Daub, Jennifer; Conlon, Claire; Maroon, Habib; Thomas, Fran; Aboobaker, Aziz; Blaxter, Mark

Contact person(s)
Blaxter, Mark
Data manager(s)
Kumar, Sujai

No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

These files accompany the peer-reviewed version of http://dx.doi.org/10.1101/033464

A previous dataset https://zenodo.org/record/45162 accompanied the version of this manuscript at BioRxiv - biorxiv.org/content/early/2015/12/13/033464

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

Abstract

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 et al (2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci USA 112:15976-15981) the authors concluded that the tardigrade Hypsibius dujardini 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 H. dujardini. As expected from whole-organism DNA sampling, our raw data contained reads from non-target genomes. Filtering using metagenomics approaches generated a draft H. dujardini 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 et al. genome derived from contaminants. We conclude that fHGT into H. dujardini 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.

 

Name Size
all.maker.proteins.edit.fasta.gz
md5:eb78ef83446804a450cd61e8fd12487d
5.1 MB Download
all.maker.transcripts.edit.fasta.gz
md5:3ae957e07cc18cce1ae09693645b656c
9.1 MB Download
HGT_phylogenetic_files.tgz
md5:fffb9901f89978ae7f263e7858825c02
208.4 kB Download
Hypsibius_dujardini_files_README.md
md5:1f07636b290b87c687cae1442019d289
7.0 kB Download
maker1.gff3.gz
md5:972642042eb35ebb04479f37c511e0cd
85.4 MB Download
nHd.1.0.BlobDB.json.gz
md5:bd22639d0b6cb7d8e49f98ff0e274dc0
11.8 MB Download
nHd.1.0.contigs.cov.fna.gz
md5:91e50953ff76979e7333bf57e233acbe
51.0 MB Download
nHd.2.3.1.aug.gff.gz
md5:559b82c7d0306d9b1ba3a6721cd7b7ec
12.6 MB Download
nHd.2.3.1.aug.proteins.fasta.gz
md5:726be5090ee70da703532f5a3ff5db83
5.3 MB Download
nHd.2.3.1.aug.transcripts.fasta.gz
md5:6d98b942de24b34338e2298dc196d1e7
8.4 MB Download
nHd.2.3.abv500.fna.gz
md5:f0399725aca42a79c9e7e6e195c318f0
31.6 MB Download
nHd.2.3.nHd_lib350-cov.BlobDB.json.gz
md5:060aa263bdd11ad185ee21a915e77977
1.6 MB Download
Supplemental_File_10_Blast2GO_results.txt
md5:73f1436e651ebd0b90aa5160557ec23b
13.7 MB Download
Supplemental_File_1_v28_2016_02_03.docx
md5:dd117d03d795fe27582d1824c75f8ad4
5.7 MB Download
supplemental_file_2_nhd23_likely_contaminant_scaffolds.txt
md5:1e3dd5a757e3106164174cdba001d9e6
1.8 kB Download
supplemental_file_3_summary_stats_from_blobplot_of_unc_tggenome.txt
md5:af3c433ff7ae40143893175b0414a6bb
6.5 kB Download
Supplemental_File_4_Assignments_of_the_6663_putative_UNC_HGT_loci.txt
md5:eb0ec20e836dbd18656dda51347cf2bc
430.3 kB Download
Supplemental_File_5_HGT_candidates_in_the_UNC_assembly_tested_by_PCR.txt
md5:7c69bae53da199c4c510bec1ae60a88f
49.7 kB Download
Supplemental_File_6_Analysis_of_Edinburgh_fHGT_candidates.txt
md5:9da0789b53db74a316a5f4e63aeadf59
140.5 kB Download
Supplemental_File_7_High_resolution_figures.pdf
md5:c8cf324e68d6b97650b486e095a4347c
410.5 MB Download
Supplemental_File_8_EST_and_GSS_accessions.txt
md5:abf21b979593545ba17fbabf9133cd39
57.4 kB Download
Supplemental_File_9_Summary_stats_from_blobplot_of_nHd23.txt
md5:43747f4d8e9fd41ae502973cf7a7fc72
4.8 kB Download
tardi_RNASeq.vs.nHd.2.3.bam.reads_cov.catcolour.txt.gz
md5:1600129c61957fb2d9102b41274dded4
46.5 kB Download
tardi_RNASeq.vs.unc.bam.reads_cov.catcolour.txt.gz
md5:e6be20593baae9876a6ac86923530026
155.9 kB Download
Trinity.fasta.c99.gz
md5:1a681de32661e434927ddd58e7eceea9
22.4 MB Download
unc.nHd-cov.uniref.nt.BlobDB.json.gz
md5:fe1a4bc4e137d637a61ebe983d1ed0b7
4.7 MB Download
unc.TG-cov.BlobDB.json.gz
md5:eb19082be7a41c4c32949be78ae77475
5.2 MB Download

Share

Cite as