The dynamic genome of Hydra

Posted: April 4, 2010 at 8:29 pm

Story Summary: Present addresses: Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK (P. A. W. ); Institute of Human Genetics, University of Heidelberg, D-69120 Heidelberg, Germany (A. -K. Here we report the genome of Hydra magnipapillataand compare it to the genomes of the anthozoan Nematostella vectensis6and other animals. Comparisons of the Hydragenome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction. The genomic basis of cnidarian evolution has so far been viewed from the perspective of an anthozoan, the sea anemone Nematostella vectensis6. Hydrais a medusozoan that diverged from anthozoans at least 540 millions year ago. We generated draft assemblies of the Hydra magnipapillatagenome using a whole-genome shotgun approach (Supplementary Information sections 1-3and Supplementary Figs 1-3). Although the sequenced strain reproduces clonally in the laboratory by asexual budding, it is diploid with substantial heterozygosity (~0. Two complementary assemblies (CA and RP) were generated (Supplementary Information section 3) and deposited in GenBank. The CA assembly gives an estimated non-redundant genome size of 1. 9Gb (see Supplementary Information section 3for a discussion of genome size calculations). 4) as expected based on the longer branch leading to Hydrain peptide-based phylogenies6. Transposable elements make up ~57% of the Hydragenome and represent over 500 different families (Supplementary Information section 9). 1and Supplementary Table 3), is a non-long-terminal-repeat (non-LTR) retroelement of the chicken repeat 1 (CR1) family. a, The top panel shows phylogenetic relationships between four Hydraspecies based on ESTs (using Nei-Gojobori synonymous substitution rates; see Supplementary Fig. The bottom panel shows the fraction of the genome that is occupied by a specific repeat class at a given divergence from the repeat consensus generated by the ReAS (recovery of ancestral sequences) algorithm (see Supplementary Information section 9). Substitution levels are corrected for multiple substitutions using the Jukes-Cantor formula K= -3/4ln(1-i4/3), where iis per cent dissimilarity on the nucleotide level from the repeat consensus. Three element expansions are inferred, the most distinct are the most ancient at ~0. b, c, Example of periods of activity of a single HydraCR1 retrotransposon family (b) and the maximum likelihood phylogeny of the family (c). Electron micrographs reveal bacterial cells underneath the glycocalyx, the coat that overlies the apical surface of the ectodermal epithelial layer of Hydra(Supplementary Fig. Our assembly yielded eight large putative bacterial scaffolds as evidenced by: (1) high G+C content (in contrast to the low G+C content of the Hydragenome); (2) no high-copy repeat sequences typical of Hydrascaffolds; and (3) closely spaced single-exon open reading frames with best hits to bacterial genes (Supplementary Information section 11, Supplementary Fig. These scaffolds span a total of 4Mb encoding 3,782 single-exon genes and represent an estimated 98% of the bacterial chromosome. 12) and conserved clusters of orthologous groups of proteins (COGs) indicate that this bacterium is a novel Curvibacterspecies belonging to the family Comamonadaceae (order Burkholderiales)11. Non-metazoan genes among cnidarian ESTs have been reported previously12, and we have now found further examples of such genes in the Hydragenome assembly. These genes are candidates for horizontal gene transfer (HGT) (Supplementary Information section 12). Of these, 51 have no blast hits to other metazoans, except in a few cases to Nematostella. Potential donors of these HGT candidates are widely distributed among different bacterial phyla (Supplementary Table 15) and show no enrichment for close relatives of Curvibacter. The HGT candidates generally have fewer introns than Hydragenes and nearly one-half are single-exon genes (Supplementary Fig. This pathway could modify endogenous glycoproteins or proteoglycans in Hydra. We also identified 90 transposable elements that were potentially horizontally transferred into the Hydragenome. Transposable elements have been shown previously to be horizontally transferred in metazoans13. With the exception of engrailed, descendants of all of the classes of homeobox genes in the megacluster are found in Nematostella16, 17. Hydrais missing a substantial fraction of megacluster descendants16, indicating secondary loss. In addition to the loss of emxand evegenes, Hydrahas undergone several other marked gene losses; for example, it lacks fluorescent protein genes and key circadian rhythm genes (Supplementary Information section 14). All major bilaterian signalling pathways, including Wnt, transforming growth factor-b, Hedgehog, receptor tyrosine kinase and Notch, are present in Hydraand Nematostella. The head organizer, which is located at the apical tip of the adult polyp, is derived from the gastrula blastopore in cnidarians. Orthologues of a number of genes known to act in the Spemann-Mangold organizer in Xenopusare present in the Hydraand Nematostellagenomes. The extracellular portions of two Hydrareceptor tyrosine kinases22, 23contain a novel protein domain, sweet tooth (SWT). The SWT domain is also present in ESTs from the hydrozoan Clytia, but is absent from all other sequenced genomes, including that of Nematostella(Supplementary Fig. SWT is among the most abundant protein domains encoded in the Hydragenome. Given its presence in receptors and secreted proteins, we deduce that the SWT domain defines a large, diverse and novel set of signalling proteins. There are two members of the Sox B group in Hydra. Studies of diverse cnidarians support this scenario (see Supplementary Information section 14for details). Both cnidarians, however, lack crucial, specific regulators associated with vertebrate striated (troponin complex) or smooth muscles (caldesmon), indicating that these specializations arose after the cnidarian-bilaterian split. Hydraalso shows secondary simplifications relative to Nematostella, which has a greater degree of muscle-cell-type specialization, including specialized retractor muscle cells. Hydralacks several components of the dystroglycan complex (/-sarcoglycan and b-sarcoglycan, /b-dystroglycan and -syntrophin), which may lead to a less robust tethering of actin to the cell membrane than in Nematostella. Similarly, the absence of a bona fide myosin light chain kinase and phosphatase in Hydraindicates a divergence or loss of regulation by myosin regulatory light chain phosphorylation. Thus, even among cnidarians, we see substantial variation in muscle-associated components superimposed on the eumetazoan core, with the Hydramuscular system representing a secondary simplification from a more complex cnidarian ancestor. 2a), and that these synapses contain dense core vesicles, paramembranous densities and cleft filaments26similar to canonical neuromuscular junctions in bilaterians. Together, these data indicate that a canonical bilaterian neuromuscular junction was probably not present in the last common ancestor of cnidarians and bilaterians. a, Electron micrograph of a nerve synapsing on a Hydraepitheliomuscular cell. Three vesicles are located in the nerve cell at the site of contact with the epitheliomuscular cell. AChE, acetylcholinesterase; ChT, choline transporter; MuSK, muscle-specific kinase; VAChT, vesicular acetylcholine transporter. High resolution image and legend (228K)Download PowerPoint slide (610K)In Hydraand Nematostella, epitheliomuscular cells have an apical junctional belt in the form of a septate junction, clear apical-basal polarity, and hemidesmosome-like contact sites with the extracellular matrix (mesoglea) on their basal surface (Fig. This indicates that the common cnidarian-bilaterian ancestor possessed a genetic inventory for the formation of all types of eumetazoan cell-cell and cell-substrate junctions. Similarly, the lack of occludin genes in cnidarians and other non-chordates (Fig. a, Schematic diagram of the positions of cell-cell and cell-matrix contacts in Hydraepitheliomuscular cells. Septate junction, red; gap junctions, green; spot desmosomes, blue; hemidesmosome-like cell-matrix contact, yellow. 18) that is able to interact with b- and p120/-catenin (Supplementary Information section 17). The sequencing of the Hydragenome has revealed unexpected relationships between the genetic makeup of the animal and its biology. Hydrahas a complete set of muscle genes but lacks mesoderm and forms muscles only in epithelial cells. TopMethods SummaryThe genome of Hydra magnipapillatastrain 105 was sequenced at the J. Craig Venter Institute using the whole genome shotgun approach. Complementary DNA libraries were prepared using standard methods and ESTs were generated at the National Institute of Genetics (Mishima, Japan) and the Genome Sequencing Center (Washington University, St Louis). ESTs have been deposited in the dbEST database at the National Center for Biotechnology Information. TopAcknowledgementsWe are grateful to S. Clifton, R. Wilson and the EST sequencing group at the Genome Sequencing Center at the Washington University School of Medicine for their efforts in generating the HydraESTs and to the National Science Foundation for its support of the HydraEST project (grant number IBN-0120591). Funding for the sequencing of the Hydragenome was provided by the National Human Genome Research Institute. D. S. R. was supported by R. Melmon and the Gordon and Betty Moore Foundation. Work at the US Department of Energy Joint Genome Institute was supported by the Office of Science of the US Department of Energy under Contract No. T. C. G. B. was supported by grants from the Deutsche Forschungsgemeinschaft (DFG SFB617-A1) and from the DFG Cluster of Excellence programs The Future Ocean and Inflammation at Interfaces. T. W. H. was supported by grants from the Deutsche Forschungsgemeinschaft including SFB488-A12 and the DFG Cluster of Excellence program CellNetworks. Support for H. W. was provided by the TOYOBO Biotechnology Foundation and the Alexander von Humboldt Foundation. (Mercator Professor) and Y. N. was provided by the Deutsche Forschungsgemeinschaft. A. C. , E. F. K. , O. S. , H. R. B. , C. N. D. , D. S. R. and R. E. S. directed the project and wrote the manuscript. D. S. R. , J. A. C. , O. S. , T. M. , D. M. G. , U. H. , T. K. , S. E. P. , S. S. and N. H. P. carried out genome assembly and gene annotation at UC Berkeley. Construction of cDNA libraries and analysis of ESTs was carried out by H. R. B. , R. E. S. , D. F. K. , S. E. H. , L. G. , D. L. , L. L. , J. P. , B. B. , P. A. W. , T. F. , C. N. -F. Remember our threads are for feedback and discussion – not for publishing papers, press releases or advertisements. 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