Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus
Yuki Yoshida , Georgios Koutsovoulos , Dominik R. Laetsch, Lewis Stevens, Sujai Kumar, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru Tomita, Mark Blaxter , Kazuharu Arakawa
Published: July 27, 2017 https://doi.org/10.1371/journal.pbio.2002266
Abstract
Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.
Author summary
Tardigrades are justly famous for their abilities to withstand environmental extremes. Many freshwater and terrestrial species can undergo anhydrobiosis—life without water—and thereby withstand desiccation, freezing, and other insults. We explored the comparative biology of anhydrobiosis in 2 species of tardigrade that differ in the mechanisms they use to enter anhydrobiosis. Using newly assembled and improved genomes, we find that Ramazzottius varieornatus, a species that can withstand rapid desiccation, differs from Hypsibius dujardini, a species that requires extended preconditioning, in not showing a major transcriptional response to anhydrobiosis induction. We identified a number of genetic systems in the tardigrades that likely play conserved, central roles in anhydrobiosis as well as species-unique components. Compared to previous estimates, our improved genomes show much reduced levels of horizontal gene transfer into tardigrade genomes, but some of the identified horizontal gene transfer (HGT) genes appear to be involved in anhydrobiosis. Using the improved genomes, we explored the evolutionary relationships of tardigrades and other molting animals, particularly nematodes and arthropods. We identified conflicting signals between sequence-based analyses, which found a relationship between tardigrades and nematodes, and analyses based on rare genomic changes, which tended to support the traditional tardigrade-arthropod link.
Citation: Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, et al. (2017) Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLoS Biol 15(7): e2002266. https://doi.org/10.1371/journal.pbio.2002266
Academic Editor: Chris Tyler-Smith, The Wellcome Trust Sanger Institute, United Kingdom of Great Britain and Northern Ireland
Received: February 20, 2017; Accepted: June 23, 2017; Published: July 27, 2017
Copyright: © 2017 Yoshida et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All raw data have been deposited in the relevant INSDC databases. The H. dujardini assembly (nHd3.1) has been deposited at DDBJ/ENA/GenBank under the accession MTYJ00000000. All mRNA-Seq data have been uploaded to GEO and SRA under the accession IDs GSE94295 and SRP098585, and the PacBio raw reads and miRNA-Seq data into SRA under the accession IDs SRX2495681 and SRX2495676. Accession IDs for each individual sequence file are given in Supplementary S1 Table. We have established a dedicated Ensembl genome browser (version 85) using the EasyImport pipeline and imported the H. dujardini genome and annotations described in this paper and the new gene predictions for R. varieornatus. These data are available to browse, query, and download at http://www.tardigrades.org.
Funding: University of Edinburgh. Baillie Gifford Studentship for LS. James Hutton Institute/School of Biological Sciences University of Edinburgh. Studentship for DRL. Japan Society for the Promotion of Science (JSPS) https://www.jsps.go.jp (grant number 22681029). Grant-in-Aid for Young Scientists for KA. BBSRC (grant number BB/K020161/1). Award for SK. Tomy Digital Biology Co., Ltd. Sequencing Grant Program For PacBio sequencing for KA. The Sumitomo Foundation http://www.sumitomo.or.jp (grant number 140340). Grant for Basic Science Research Projects for KA. Yamagata Prefectural Government and Tsuruoka City, Japan. Funding for KA and MT. BBSRC (grant number COD17089). PhD studentship for GK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: AMPK, 5' adenosine monophosphate-activated protein kinase; API, application-programming interface; ATM, ataxia-telangiectasia mutated; ATR, ataxia telangiectasia and Rad3-related protein; BER, base excision repair; BLAST, Basic Local Alignment Search Tool; BSC1, bypass of stop codon protein 1; BUSCO, Benchmarking Universal Single-Copy Orthologs; CAHS, cytosolic abundant heat soluble; CaM, calmodulin; CASP, caspase; CATE, catalase; CBF, C-repeat-binding factor; CDS, coding sequence; CEGMA, Core Eukaryotic Genes Mapping Approach; CHK, checkpoint kinase; CNG, cyclic nucleotide-gated channel; Dsup, damage suppressor; EGF, epidermal growth factor; GPCR, G-protein-coupled receptor; GST, glutathione S-transferase; GTP, guanosine-5'-triphosphate; GTR+G, General Time Reversible model with Gamma distribution of rates model; GTR-CAT+G, GTR plus rate categories model; HGT, horizontal gene transfer; HR, homologous recombination; HSP, heat shock protein; INSDC, International Nucleotide Sequence Database Collaboration; IPR, InterPro domain identifier; KAAS, KEGG Automatic Annotation Server; KEGG, Kyoto Encyclopedia of Genes and Genomes; LDL, low-density lipoprotein; MAHS, mitochondrial abundant heat soluble protein; MCL, Markov Cluster Algorithm; miRNA-Seq, microRNA sequencing; MMR, mismatch repair; mTOR, mechanistic target of rapamycin; NER, nucleotide excision repair; NHEJ, nonhomologous end joining; PacBio, Pacific Biosciences; PARP, poly(ADP-ribose) polymerase; PF, PFam identifier; PHD, plant homeodomain; RAxML, Randomized Axelerated Maximum Likelihood; RH, relative humidity; RNAi, RNA interference; RNA-Seq, RNA sequencing; ROS, reactive oxygen species; RyLEAM, late embryogenesis abundant protein mitochondrial; SAHS, secretory abundant heat soluble; SIRT1, sirtuin 1; SOD, superoxide dismutase; SRA, Sequence Read Archive; TPM, transcript(s) per million; TPS, trehalose-6-phosphatase synthase; TSC1/2, tuberous sclerosis 1/2; UDP, uridine diphosphate; UGT, UDP-glucuronosyltransferase; VHL, von Hippel-Lindau tumor suppressor
FREE PDF GRATIS: PLoS Biology
