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Subject terms: Genetics
日本語要約
The genomes of four tapeworm species reveal adaptations to
parasitism
Isheng J. Tsai, Magdalena Zarowiecki, Nancy Holroyd, Alejandro Garciarrubio, Alejandro Sanchez-Flores, Karen L.
Brooks, Alan Tracey, Raúl J. Bobes, Gladis Fragoso, Edda Sciutto, Martin Aslett, Helen Beasley, Hayley M. Bennett,
Jianping Cai, Federico Camicia, Richard Clark, Marcela Cucher, Nishadi De Silva, Tim A. Day, Peter Deplazes, Karel
Estrada, Cecilia Fernández, Peter W. H. Holland, Junling Hou, Songnian Hu et al.
Nature 496, 57–63 (04 April 2013) doi:10.1038/nature12031
Received 09 November 2012 Accepted 21 February 2013 Published online 13 March 2013
Abstract
Tapeworms (Cestoda) cause neglected diseases that can be fatal and are difficult to treat, owing to inefficient drugs. Here we
present an analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E.
granulosus, Taenia solium and the laboratory model Hymenolepis microstoma as examples. The 115- to 141-megabase
genomes offer insights into the evolution of parasitism. Synteny is maintained with distantly related blood flukes but we find
extreme losses of genes and pathways that are ubiquitous in other animals, including 34 homeobox families and several
determinants of stem cell fate. Tapeworms have specialized detoxification pathways, metabolism that is finely tuned to rely on
nutrients scavenged from their hosts, and species-specific expansions of non-canonical heat shock proteins and families of
known antigens. We identify new potential drug targets, including some on which existing pharmaceuticals may act. The
genomes provide a rich resource to underpin the development of urgently needed treatments and control.
Introduction
Echinococcosis (hydatid disease) and cysticercosis, caused by the proliferation of larval tapeworms in vital organs1, are
among the most severe parasitic diseases in humans and account for 2 of the 17 neglected tropical diseases prioritized by the
World Health Organization2. Larval tapeworms can persist asymptomatically in a human host for decades3, eventually causing
a spectrum of debilitating pathologies and death1. When diagnosed, the disease is often at an advanced stage at which
surgery is no longer an option4. Tapeworm infections are highly prevalent worldwide5, and their human disease burden has
been estimated at 1 million disability-adjusted life years, comparable with African trypanosomiasis, river blindness and dengue
fever. Furthermore, cystic echinococcosis in livestock causes an annual loss of US$2 billion6.
Tapeworms (Platyhelminthes, Cestoda) are passively transmitted between hosts and parasitize virtually every vertebrate
species7. Their morphological adaptations to parasitism include the absence of a gut, a head and light-sensing organs, and
they possess a unique surface (tegument) that is able to withstand host-stomach acid and bile but is still penetrable enough to
absorb nutrients7.
Tapeworms are the only one of three major groups of worms that parasitize humans, the others being flukes (Trematoda) and
round worms (Nematoda), for which no genome sequence has been available so far. Here we present a high-quality reference
tapeworm genome of a human-infective fox tapeworm Echinococcus multilocularis. We also present the genomes of three
other species, for comparison; E. granulosus (dog tapeworm), Taenia solium (pork tapeworm), both of which infect humans,
and Hymenolepis microstoma (a rodent tapeworm and laboratory model for the human parasite Hymenolepis nana). We have
mined the genomes to provide a starting point for developing urgently needed therapeutic measures against tapeworms and
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other parasitic flatworms. Access to the complete genomes of several tapeworms will accelerate the pace at which new tools
and treatments to combat tapeworm infections can be discovered.
The genomes and genes of tapeworms
The E. multilocularis genome assembly was finished manually (Supplementary Information, section 2), producing a high-quality
reference genome in which 89% of the sequence is contained in 9 chromosome scaffolds that have only 23 gaps
(Supplementary Table 1.2). One chromosome is complete from telomere to telomere, and 13 of the expected 18 telomeres are
joined to scaffolds (Fig. 1a). This quality and completeness is comparable to that of the first publications of Caenorhabditis
elegans and Drosophila melanogaster genomes8, 9. The 115- to 141-megabase (Mb) nuclear tapeworm genomes were
sequenced using several high-throughput technologies (Supplementary Table 1.1). The tapeworm genomes are
approximately one-third of the size of the genome of their distant flatworm relative, the blood fluke Schistosoma mansoni10,
mainly because it has fewer repeats (Supplementary Information, section 3). By sequencing several isolates of E. multilocularis
(Supplementary Table 3.2), we revealed tetraploidy in protoscoleces of one isolate, and a trisomy of chromosome 9 (the
smallest chromosome, and possibly the only one for which a trisomy is tolerated) transiently exhibited in protoscoleces and
metacestodes from two different isolates (Fig. 1c, d and Supplementary Figs 3.1, 3.2 and 3.3), consistent with previous
observations of karyotype plasticity in flatworms11.
Figure 1: Genome of E. multilocularis.
a, The nine assembled chromosomes (Chr 1–Chr 9) of E. multilocularis with telomeres (red dots). Physical gaps in the sequence
assembly (white boxes with blue dot beneath) are bridged by optical map data. Each colour segment is defined as an array of at least
three genes that each has a single orthologous counterpart on one S. mansoni chromosome, regardless of their locations on the
chromosome. b, One-to-one orthologues connecting E. multilocularis and S. mansoni chromosomes. c, Distribution of normalized
genome coverage on isolate GT10/2. Each horizontal line depicts median coverage of 100-kb windows normalized against the mean
coverage for the genome (130×). Even coverage was observed across the first eight chromosomes, but 1.5× coverage of chromosome 9
indicates trisomy. Similar plots for other isolates are shown in Supplementary Fig. 3.1. d, Distribution of minor allele frequency (MAF) of
heterozygous sites in five isolates of E. multilocularis (plot for individual isolates in Supplementary Fig. 3.1), identified by mapping
sequencing reads against the assembled chromosome consensus sequences. At each site, the proportion of bases that disagree with
the reference is counted. For four isolates, the MAF peaks at around 0.5, indicative of diploidy, whereas JAVA05/1 peaks at 0.25,
suggesting tetraploidy. Chromosome 9 of GT10/2 is plotted separately (marked by asterisk) from chromosomes 1 to 8, and the MAF
display a clear departure of 0.5 and peaks around 0.33, consistent with a trisomy.
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Aided by deep transcriptome sequencing from multiple life-cycle stages, we identified 10,231 to 12,490 putative genes per
genome (Supplementary Table 5.5). Similar to the genome of S. mansoni12, distinct ‘micro-exon genes’ are present in
tapeworm genomes, with multiple internal exons that are small (typically less than 36 bases) and divisible by 3 (Supplementary
Information, section 5). To identify gene gain and loss in tapeworms, orthologous relationships were predicted between
tapeworms and eight other species (Fig. 2). Although gene order has been lost, ancient chromosomal synteny is preserved
among parasitic flatworms (Fig. 1b and Supplementary Table 7.3). Two chromosomes in E. multilocularis (Fig. 1a, b)
correspond to the S. mansoni Z sex chromosome. Schistosomes are unusual among flatworms in that they have sexual
dimorphism, but how common ancestors of both tapeworms and flukes evolved into female-heterogametic parasites, like S.
mansoni, remains to be elucidated.
Figure 2: Evolution of tapeworm parasitism.
Phylogeny of the main branches of Bilateria; Ecdysozoa (including fruitflies and nematodes), Deuterostomia (including lancelet,
zebrafish, mice and humans), and Lophotrochozoans (including Platyhelminthes (flatworms)) (based on phylogeny in Supplementary
Fig. 7.1). The gains and losses of life-cycle traits for these parasitic flatworms include the evolution of endoparasitism (a), passive
transmission between hosts (b), acquisition of vertebrate intermediate host (c), ability to proliferate asexually in intermediate host (d).
Morphological traits that have evolved include the loss of eye cups (e), gain of neodermatan syncytial epithelia (f), loss of gut (g),
segmentation of body plan (h), and changes in the laminated layer (to contain specialized apomucins; i). Gains and losses of genomic
traits include spliced-leader trans-splicing (1), loss of Wnt genes (2), loss of NEK kinases, fatty acid biosynthesis and ParaHox genes
(3), anaerobic metabolic ability through the malate dismutation/rodhoquinone pathway, merger of glutaredoxin and thioredoxin reductase
to thioredoxin glutathione reductase (TGR) (4), evolution of tapeworm- and fluke-specific Argonaute (Ago) family, micro exon genes
(MEGs) and PROF1 GPCRs (5), loss of peroxisomal genes (6), and complete loss of vasa, tudor and piwi genes, NF-κB pathway, loss
of 24 homeobox gene families (indicated by ‘H’), metabolic proteases and amino acid biosynthesis (7). In tapeworms, gains and losses
of genomic traits include innovation of bimodal intron distribution and novel fatty acid transporters (8), expansion of mu-class glutathione
S-transferases, GP50 antigens and tetraspanins (9), loss of the molybdopterin biosynthesis pathway, loss of 10 homeobox gene
families (10), fewer GPCRs and fewer neuropeptides encoded by each protopeptide (11), and expansion of heat shock proteins (Hsp)
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and species-specific antigens (12).
Genome-wide identification of polycistrons in tapeworms shows that there are 308 putative polycistrons in E. multilocularis, with
the largest containing 4 genes. The internal gene order within E. multilocularis polycistrons is largely the same as in T. solium
and H. microstoma (Supplementary Table 6.5), and—to some extent—as in flukes; 39% of S. mansoni orthologues of genes
within E. multilocularis polycistrons retain colinearity. Of these S. mansoni genes, 40% have transcriptome evidence
supporting their polycistronic transcription10, demonstrating further that gene order in polycistrons is highly conserved over
long evolutionary time13 (P < 0.0001, Supplementary Information, section 6).
Polycistrons are resolved into individual coding transcripts using spliced-leader trans-splicing, but spliced-leader trans-splicing
also occurs in genes outside of polycistrons. Using deep transcriptome sequencing (RNA-seq) we found evidence of splicedleader
trans-splicing in approximately 13% of E. multilocularis genes (Supplementary Table 6.2), less than the 70% observed
in C. elegans14 and 58% in a tunicate15.
Specialized metabolism and detoxification
The high-confidence gene sets reveal extensive reductions in overall metabolic capability and an increased ability to absorb
nutrients, compared to that of other animals (Figs 2 and 3, and Supplementary Information, section 9). Their main energy
source, carbohydrates, can be catabolized by aerobic respiration or by two complementary anaerobic pathways; the lactate
fermentation and malate dismutation pathways. The parasiticidal effects of mitochondrial fumarate reductase inhibitors have
been demonstrated in vitro, suggesting that the malate dismutation pathway would be an effective target for the development
of novel therapeutics16.
Figure 3: Conservation of individual metabolic pathways.
Heatmap showing the conservation of individual metabolic pathways for E. multilocularis (Em), E. granulosus (Eg), T. solium (Ts), H.
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microstoma (Hm) and S. mansoni (Sm) compared to those of humans (Hs) and mice (Mm). Each row indicates an individual metabolic
pathway grouped by their superclass membership (defined by KEGG (Kyoto Encyclopedia of Genes and Genomes)). Coloured tiles
indicate the level of conservation (percentage of enzymes detected) of each pathway within each species. KEGG pathways with
insufficient evidence (that is, containing only one enzyme) in E. multilocularis have been removed. CoA, coenzyme A; EC, enzyme
commission number; TCA, tricarboxylic acid cycle.
Tapeworms, like flukes, lack the ability to synthesize fatty acids and cholesterol de novo17, 18. Instead, they scavenge
essential fats from the host using fatty acid transporters and lipid elongation enzymes (Supplementary Table 9.2), as well as
several tapeworm-specific gene families, such as fatty acid binding protein (FABP) and the apolipoprotein antigen B
(Supplementary Information, section 8). Uptake of fatty acids seems to be crucial in Echinococcus spp. metacestodes, in which
both FABP and antigen B gene families are among the most highly expressed genes19 (Supplementary Table 5.7).
Tapeworms and flukes have lost many genes associated with the peroxisome (Supplementary Information, section 8), an
organelle in which fatty acid oxidation occurs, and may lack peroxisomes altogether, as seen in several other parasites20.
Compared with other animals, S. mansoni has a reduced ability to synthesize amino acids17. In tapeworms, this capacity is
reduced further, with serine and proline biosynthesis enzymes absent from E. multilocularis (Fig. 3 and Supplementary
Information, section 9). Many enzymes in the molybdopterin biosynthesis pathway seemed to be lost in tapeworms, along with
enzymes that use molybdopterin as a cofactor. The ability to utilize molybdenum in enzymatic reactions was believed to be
present in all animals21, but has been lost in some eukaryotic parasites22.
Differences in the detoxification systems between tapeworms and their mammalian hosts may be exploited for drug design
(Supplementary Information, section 9). We found that, like flukes23, tapeworms typically have only one cytochrome P450
gene, suggesting that their ability to oxidize many xenobiotics and steroids is substantially lower than that of their hosts.
Uniquely, tapeworms and flukes have merged two key enzymatic functions for redox homeostasis in one single enzyme:
thioredoxin glutathione reductase (TGR). TGR is an essential gene and validated drug target in flukes24. Downstream of TGR
we find an unexpected diversity of thioredoxins, glutaredoxins and mu-class glutathione S-transferases (GSTs)
(Supplementary Table 9.3). The GST expansion suggests that tapeworms would be able to water-solubilize and excrete a large
range of hydrophobic compounds, which may add complexity to the pharmacokinetics of drugs.
Homeobox gene loss
Homeobox genes are high-level transcription factors that are implicated in the patterning of body plans in animals. Across
parasitic flatworms, the homeobox gene numbers are extensively reduced (Supplementary Table 10.1). Most bilaterian
invertebrates have a conserved set of approximately 100 homeobox genes (for example, 92 conserved in C. elegans, 102 in D.
melanogaster, and 133 in the lancelet) 25. Of the 96 homeobox gene families that are thought to have existed at the origin of
the Bilateria, 24 are not present in tapeworms and flukes, and a further 10 were lost in tapeworms, making their complement by
far the most reduced of any studied bilaterian animal25. Among the tapeworm-specific gene losses are gene families involved
in neural development (mnx, pax3/7, gbx, hbn and rax). This is somewhat surprising considering that tapeworms possess a
well-developed nervous system, albeit with reduced sensory input and cephalization. Tapeworms also lack the ParaHox genes
(gsx, pdx, cdx) ancestrally involved in specification of a through-gut26, 27, although these seem to have been lost before the
tapeworm gut was lost. Other conserved genes found in bilaterian developmental pathways such as Hedgehog and Notch
were found to be present and intact, although the Wnt complement is greatly reduced compared to the ancestral (spiralian)
complement of 12 Wnt ligands28 (Supplementary Table 10.2).
Stem cell specializations
Extreme regenerative capability and developmental plasticity, mediated by ever-present somatic stem cells (neoblasts), have
made flatworms popular models for stem cell research29. All multicellular organisms rely on stem cells for proliferation and
growth, so it is remarkable that tapeworms and flukes appear to lack the ubiquitous stem cell marker gene vasa
(Supplementary Information, section 11). Instead tapeworms have two copies of another dead-box helicase (PL10), which we
propose may have taken over some of the functions of vasa (Supplementary Fig. 11.1). Tapeworms and flukes are also
missing the piwi gene subfamily and piwi-interacting tudor-domain containing proteins. The piwi genes belong to a subfamily of
genes encoding argonaute proteins, and we also found that tapeworms have a new subfamily of argonaute proteins
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(Supplementary Fig. 11.2) that may bind a newly discovered potential small RNA precursor30. Both piwi and vasa are usually
essential in regulating the fate of germline stem cells in animals, and vasa suppression usually leads to infertility or death31.
These findings suggest that stem-cell-associated pathways in parasitic flatworms may be highly modified.
Specialization of the tapeworm proteome
We sought to identify novel and expanded gene families in tapeworms, and found many frequently occurring novel domains
involved in cell–cell adhesion and the formation of the tegument (Supplementary Information, section 8). For example, several
novel domains are found on the ectodomain of cadherins (Supplementary Information, section 8), and tapeworms have
proportionally more tetraspanin copies (30–36) (Supplementary Table 12.1) than the highly expanded repertoires of fruitflies
and zebrafish32. The acellular carbohydrate-rich laminated layer, which coats the outside of Echinococcus metacestodes, is a
unique genus-specific trait and one of the few morphological traits that differ between the very closely related species E.
granulosus and E. multilocularis. We identified corresponding species differences in an Echinococcus-specific apomucin family
(Supplementary Fig. 12.1), an important building block of the laminated layer33. One particular copy is highly differentiated
between the two species (non-synonymous to synonymous substitution ratio of >1) and is the fifth most highly expressed in the
metacestode stage of E. multilocularis (Supplementary Table 5.7). Galactosyltransferases that probably decorate the
apomucins with galactose residues, the predominant sugar of laminated layer glycans, are similarly diverged33
(Supplementary Information, section 8). Approximately 20% of the genes are exclusive to tapeworms, and these include many
highly expressed antigen families, such as antigen B, the glycosylphosphatidylinositol (GPI)-anchored protein GP50 (ref. 34),
and the vaccine target EG95 (ref. 35) (Supplementary Table 12.4).
One of the most striking gene family expansions in the tapeworm genomes is the heat shock protein 70 (Hsp70) family.
Phylogenetic analysis revealed independent and parallel expansions in both the Hsp110 and the cytosolic Hsp70 clades (Fig.
4). Several examples of expansions exist at various clades of Hsp70 in other systems, including Hsp110 expansions in oysters
(to cope with temperature) and in cancer cells (to cope with proteotoxic stress)36, 37. Echinococcus and T. solium have the
highest number of gene expansions in the cytosolic Hsp70 clade. These expansions seem to have occurred independently in
each species, and have resulted in 22 to 32 full copies in each species (Echinococcus and T. solium) compared to 6 copies in
fruitflies and 2 in humans (Fig. 4). This expanded clade lacks classical cytosolic Hsp70 features (a conserved EEVD motif for
substrate binding and a GGMP repeat unit), and whereas the canonical cytosolic hsp70 genes are constitutively expressed in
different life-cycle stages, the non-canonical genes show almost no expression, suggesting a putative contingency role in
which individual copies of the expanded family are only highly expressed under certain conditions (Supplementary Fig. 12.2).
At least 40% of E. multilocularis hsp70-like genes are found within the subtelomeric regions of chromosomes, including the
extreme case of chromosome 8 in which eight copies (including pseudogenes) are located in the subtelomere (Supplementary
Table 12.2). No other genes are over-represented in these regions. Although Hsp70 proteins have been found in excretory–
secretory products of tapeworms38, it remains to be determined whether the non-canonical Hsps have a host-interacting role
or whether telomere proximity is important for their function or expression.
Figure 4: Heat shock protein 70 expansions in tapeworms.
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Rooted tree of Hsp70 sequences from tapeworms and the eight comparator species used in this study, with additional sequences from
baker’s yeast Saccharomyces cerevisiae, and the Pacific oyster Crassostrea gigas (a non-flatworm example of a lophotrochozoan with
a recently reported Hsp70 expansion). Different Hsp70 subfamilies are shown in different colours. Dotted red lines, E. multilocularis
hsp70 genes that are located in the subtelomeres. EEVD, the conserved carboxy-terminal residues of a canonical cytosolic Hsp70; ER
Hsp70, endoplasmic reticulum Hsp70.
Novel drug targets
Tapeworm cysts are treated by chemotherapy or surgical intervention depending on tapeworm species, patient health and the
site of the cyst. The only widely used drugs to treat tapeworm cysts are benzimidazoles39 that, owing to considerable side
effects, are administered at parasitistatic rather than parasiticidal concentrations40. Novel targets and compound classes are
therefore urgently needed.
To identify new potential drug targets, we surveyed common targets of existing pharmaceuticals; kinases, proteases, Gprotein-coupled
receptors (GPCRs) and ion channels41. We identified approximately 250 to 300 new protein kinases
(Supplementary Table 13.1), and these cover most major classes (Supplementary Information, section 13). We also identified
151 proteases and 63 peptidase-like proteins in E. multilocularis, a repertoire of similar diversity to S. mansoni, and found that,
like S. mansoni, E. multilocularis has strongly reduced copy numbers compared to those of other animals (Supplementary
Table 13.9). Many successful anthelminthic drugs target one of several different forms of neural communication41. We
therefore mapped the signalling pathways of the serotonin and acetylcholine neurotransmitters, predicted conserved and
novel neuropeptides (Supplementary Table 13.6), and classified more than 60 putative GPCRs (Supplementary Table 13.2)
and 31 ligand-gated ion channels (Supplementary Table 13.4). A voltage-gated calcium channel subunit42—the proposed
target of praziquantel—is not expressed in cysts and thus provides a putative explanation for the drug’s low efficacy.
We searched databases for potential features for target selection, including compounds associated with protein targets and
expression in the clinically relevant metacestode life-stage, and using this information we assigned weights to rank the entire
proteomes (Supplementary Table 13.10). We identified 1,082 E. multilocularis proteins as potential targets, and of these,
150 to 200 with the highest scores have available chemical leads (known drug or approved compounds).
Acetylcholinesterases, which are inhibited by mefloquine (an anti-malarial that reduces egg production in S. mansoni), are
high on the list of potential targets43. However, acetylcholinesterase transcription in tapeworm cysts is low, possibly limiting
their suitability. After filtering to remove targets with common substrates rather than inhibitors, the top of the list includes
several homologues of targets for cancer chemotherapy, including casein kinase II, ribonucleoside reductase, UMP–CMP
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kinase and proteasome subunits (Table 1). The challenges of inhibiting cancer tumours and metacestodes (particularly those
of E. multilocularis) with drugs are in some ways similar; both show uncontrolled proliferation, invasion and metastasis, and are
difficult to kill without causing damage to the surrounding tissue. Therefore, metacestodes may be vulnerable to similar
strategies as cancer; suppression of mitosis, induction of apoptosis and prevention of DNA replication. In fact, the
anthelminthic medicines niclosamide, mebendazole and albendazole have already been shown to inhibit cancer growth44.
Table 1: Top 20 promising targets in E. multilocularis
Conclusion
Tapeworms were among the first known parasites of humans, recorded by Hippocrates and Aristotle in ~300 BC (ref. 45), but a
safe and efficient cure to larval tapeworm infection in humans has yet to be found. These genomes provide hundreds of
potential drug targets that can be tested using high-throughput drug screenings that were made possible by recent advances
in axenic and cell culturing techniques39, 46, 47. Flatworms display an unusually high degree of developmental plasticity. In this
study, the high level of sequence completion enabled both gene losses and gains to be accurately determined, and has
shown how this plasticity has been put to use in the evolution of tapeworms.
Methods
Genome sequencing was carried out using a combination of platforms. RNA sequencing was performed with Illumina RNA-seq
protocols (for E. multilocularis, E. granulosus and H. microstoma) or capillary sequencing of full-length complementary DNA
libraries (T. solium). The complete genome annotation is available at http://www.genedb.org. The tapeworm genome projects
were registered under the INSDC project IDs PRJEB122 (E. multilocularis), PRJEB121 (E. granulosus), PRJEB124 (H.
microstoma) and PRJNA16816 (T. solium). Sequence data for T. solium isolate (from Mexico) were used for all orthologue
comparisons, but results relating to gene gains and losses were reconciled against an additional sequenced isolate from
China (unpublished). All experiments involving jirds (laboratory host of E. multilocularis) were carried out in accordance with
European and German regulations relating to the protection of animals. Ethical approval of the study was obtained from the
ethics committee of the government of Lower Franconia (621-2531.01-2/05). Experiments with dogs (host of E. multilocularis
sample RNA-seq ERS018054) were conducted according to the Swiss guidelines for animal experimentation and approved by
the Cantonal Veterinary Office of Zurich prior to the start of the study, and were carried out with facility-born animals at the
experimental units of the Vetsuisse Faculty in Zurich (permission numbers 40/2009 and 03/2010). A licensed hunter hunted
the fox (host of E. multilocularis sample RNA-seq ERS018053) during the regular hunting season. Hymenolepis parasites were
reared using laboratory mice in accordance with project license PPL 70/7150, granted to P.D.O. by the UK Home Office.
Accession codes
Primary accessions
E-ERAD-50
E-ERAD-56
ArrayExpress
ERP000351
ERP000452
PRJNA16816
European Nucleotide Archive
EL740221
EL763490
Expressed Sequence Tag Database
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Acknowledgements
We thank M. Dunn and OpGen for the E. multilocularis optical map; Roche for 20kb 454 libraries; R. Rance, M. Quail, D.
11.11.13 The genomes of four tapeworm species reveal adaptations to parasitism : Nature : Nature Publishing Group
www.nature.com/nature/journal/v496/n7443/full/nature12031.html 11/14
Willey, N. Smerdon and K. Oliver for sequencing libraries at WTSI; T. D. Otto for bioinformatics expertise; R. Davies and Q. Lin
for help with data release; A. Bateman, M. Punta, P. Cogghill and J. Minstry of Pfam; N. Rowlings from MEROPS database, J.
Gough at SUPERFAMILY and C. Dessimoz for OMA; C. Seed and F. Jarero for laboratory assistance; J. Overington and B. AlLazikani;
and B. Brejová for predicting genes with ExonHunter. P.D.O. and N.P.S. were supported in part by a BBSRC grant
(BBG0038151) to P.D.O. P.D.O. and Ma.Z. were supported by a SynTax joint UK Research Council grant. The European
Research Council supported P.W.H.H. and J.Paps. J.Parkinson and S.S.H. were supported by an operating grant from the
Canadian Institute for Health Research (CIHR MOP#84556). G.S. was supported by FIRCA-NIH (grant TW008588) and the
Universidad de la República, CSIC (grant CSIC 625). The E. multilocularis, E. granulosus and H. microstoma genome projects
were funded by the Wellcome Trust through their core support of the Wellcome Trust Sanger Institute (grant 098051). K.B.
was supported by a grant from the Deutsche Forschungsgemeinschaft (DFG; BR2045/4-1). The Taenia solium Genome
Project (IMPULSA 03) was supported by the Universidad Nacional Autonóma de México. The Taenia solium Genome
Consortium thanks P. de la Torre, J. Yañez, P. Gaytán, S. Juárez and J. L. Fernández for technical support; L. Herrera-Estrella
and LANGEBIO, CINVESTAV-Irapuato and C. B. Shoemaker for sequencing support and other advice; and J. Watanabe
(deceased), S. Sugano and Y. Suzuki for the construction and sequencing of the full-length cDNA library.
Author information
These authors contributed equally to this work.
Isheng J. Tsai, Magdalena Zarowiecki, Nancy Holroyd & Alejandro Garciarrubio
Affiliations
Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
1SA, UK
Isheng J. Tsai, Magdalena Zarowiecki, Nancy Holroyd, Alejandro Sanchez-Flores, Karen L. Brooks, Alan Tracey, Martin Aslett,
Helen Beasley, Hayley M. Bennett, Richard Clark, Nishadi De Silva, Thomas Huckvale, Jacqueline A. Keane, Olivia Lambert,
Sarah Nichol & Matthew Berriman
Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki
889-1692, Japan
Isheng J. Tsai
Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México
Alejandro Garciarrubio, Alejandro Sanchez-Flores, Karel Estrada & Xavier Soberón
Institute of Biomedical Research, Universidad Nacional Autónoma de México, 04510 México D.F., México
Raúl J. Bobes, Gladis Fragoso, Edda Sciutto & Juan P. Laclette
State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu
Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 1 Xujiaping,
Chengguan District, Lanzhou 730046, Gansu Province, China
Jianping Cai, Junling Hou, Xuenong Luo, Yadong Zheng & Xuepeng Cai
Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de
Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET). Facultad de Medicina, Paraguay 2155,
C1121ABG Buenos Aires, Argentina
Federico Camicia, Marcela Cucher, Laura Kamenetzky, Natalia Macchiaroli & Mara Rosenzvit
Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, USA
Tim A. Day
Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, CH-8057 Zürich,
Switzerland
Peter Deplazes
11.11.13 The genomes of four tapeworm species reveal adaptations to parasitism : Nature : Nature Publishing Group
www.nature.com/nature/journal/v496/n7443/full/nature12031.html 12/14
Cátedra de Inmunologá, Facultad de Quámica, Universidad de la República. Avenida Alfredo Navarro 3051, piso 2,
Montevideo, CP 11600, Uruguay
Cecilia Fernández & Gustavo Salinas
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Peter W. H. Holland & Jordi Paps
Beijing Institute of Genomics, Chinese Academy of Sciences, No.7 Beitucheng West Road, Chaoyang District,
Beijing 100029, China
Songnian Hu, Kan Liu & Yingfeng Luo
Department of Biochemistry & Molecular and Medical Genetics, University of Toronto, Program in Molecular
Structure and Function, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
Stacy S. Hung & John Parkinson
University of Würzburg, Institute of Hygiene and Microbiology, D-97080 Würzburg, Germany
Ferenc Kiss, Uriel Koziol & Klaus Brehm
Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
Natasha Pouchkina-Stantcheva, Nick Riddiford & Peter D. Olson
Department of Zoology, School of Natural Sciences and Regenerative Medicine Institute (REMEDI), National
University of Ireland Galway, University Road, Galway, Ireland
Nick Riddiford
Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary T2N
4Z6, Canada
James D. Wasmuth
Institute of Parasitology, McGill University, 2111 Lakeshore Road, Ste Anne de Bellevue, Quebec H9X 3V9, Canada
Mostafa Zamanian
Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809 Col. Arenal Tepepan, Delegación Tlalpan, 14610
México, D.F., México
Xavier Soberón
Institute of Biotechnology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, México.
$affiliationAuthor
Institute of Biomedical Research, Universidad Nacional Autónoma de México, 04510 México, D.F. Mexico.
$affiliationAuthor
Genomic Sciences Center, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
$affiliationAuthor
Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809 Col. Arenal Tepepan, Delegación Tlalpan, 14610
México, D.F. México.
$affiliationAuthor
School of Medicine, Universidad Nacional Autónoma de México, 04510 México, D.F. Mexico.
$affiliationAuthor
School of Sciences, Universidad Nacional Autónoma de México, 04510 México, D.F. Mexico.
$affiliationAuthor
11.11.13 The genomes of four tapeworm species reveal adaptations to parasitism : Nature : Nature Publishing Group
www.nature.com/nature/journal/v496/n7443/full/nature12031.html 13/14
Consortia
The Taenia solium Genome Consortium
Alejandro Garciarrubio, Raúl J. Bobes, Gladis Fragoso, Alejandro Sánchez-Flores, Karel Estrada, Miguel A. Cevallos, Enrique
Morett, Víctor González, Tobias Portillo, Adrian Ochoa-Leyva, Marco V. José, Edda Sciutto, Abraham Landa, Lucía Jiménez,
Víctor Valdés, Julio C. Carrero, Carlos Larralde, Jorge Morales-Montor, Jorge Limón-Lason, Xavier Soberón & Juan P. Laclette
Contributions
I.J.T., Ma.Z., N.H. and M.B. Wrote the manuscript; M.B., K.B., J.P.L., X.S. and X.C. conceived and designed the project; N.H.,
M.B. and Ma.Z. coordinated the project. R.J.B., P.D., C.F., T.H., J.H., K.L., X.L., S.H., N.M., P.D.O., M.R., E.S., N.P.S., Y.Z. and
K.B. prepared parasite material and nucleic acids; I.J.T., Ma.Z., A.G., K.E. and A.S.F. were involved in genome assembly;
I.J.T., K.L.B., A.T., H.B., S.N., T.H., A.G. and K.E. were involved in genome assembly improvement; I.J.T., Ma.Z., A.S.F., X.S.,
K.L., J.H., A.G. and K.E. were involved in gene predictions; I.J.T., Ma.Z., K.L.B., A.T., H.B., O.L., S.N., R.C., R.J.B., G.F., E.S.,
X.S., J.P.L., K.L., J.H., A.G., K.E., S.H. and X.C. were involved in gene annotation; N.D.S., M.A., J.A.K., K.E., J.H., S.H., X.S. and
Y.Z. were involved in data processing, computational and bioinformatics support; I.J.T. analysed genome structure,
comparative genomics and ploidy; A.S.F., I.J.T. and Ma.Z. analysed gene structure; T.H. and H.M.B. experimentally validated
micro-exons; A.G., K.B., F.K. and I.J.T. were involved with trans-splicing and polycistrons; I.J.T., S.S.H., J.Parkinson, G.S. and
Ma.Z. examined metabolism and detoxification; P.W.H.H., J.Paps, N.R. and P.D.O. examined homeobox gene loss; K.B., I.J.T.
and Ma.Z. examined stem cell specializations; Ma.Z. and J.D.W. examined domains; I.J.T., Ma.Z., C.F. and G.S. examined
tapeworm-specific genes and expansions; Ma.Z. examined kinases and proteases; T.A.D. and Mo.Z. examined GPCRs; Mo.Z.,
T.A.D., U.K. and K.B. examined neuropeptides; M.R., L.K., F.C. and M.C. examined neuronal signalling; Ma.Z. examined drug
targets; and G.S., M.R., C.F., K.B., P.W.H.H., P.D.O., A.G., R.J.B., G.F., E.S., X.S., J.P.L. and J.C. commented on the
manuscript drafts.
Competing financial interests
The authors declare no competing financial interests.
Corresponding authors
Correspondence to: Matthew Berriman or Klaus Brehm or $affiliationAuthor or Juan P. Laclette
The tapewormgenome projects were registered under the INSDC project IDs PRJEB122 (E. multilocularis), PRJEB121 (E.
granulosus), PRJEB124 (H. microstoma) and PRJNA16816 (T. solium, Mexico). Illumina and 454 data are released to the
European Nucleotide Archive (http://www.ebi.ac.uk/ena/) under accession numbers ERP000351, ERP000452 and
PRJNA16816. Capillary data is at http://www.ncbi.nlm.nih.gov/Traces/trace.cgi, SEQ_LIB_ID 98488, 98489 and 101760,
CENTER NAME SC (E. multilocularis) and sg1, sg2, sg3, sg4 and sg5 (T. solium, Mexico). Genome data are available from
http://www.sanger.ac.uk/resources/downloads/helminths/ (E. multilocularis, E. granulosus and H. microstoma) and
http://www.taeniasolium.unam.mx/taenia/ (T. solium). The complete genome annotation is available at http://www.genedb.org.
All RNA-seq data were released to ArrayExpress under accession numbers E-ERAD-50 or E-ERAD-56. T. solium EST
sequences were released to http://www.ncbi.nlm.nih.gov/nucest/, under accession numbers EL740221 to EL763490.
Supplementary information
PDF files
1. Supplementary Information (7.7 MB)
This file contains Supplementary Text Sections 1-13, Supplementary Figures and Supplementary References – see
contents for details.
Excel files
1. Supplementary Tables (6 MB)
This file contains Supplementary Tables 1-13.
2. Supplementary Tables (4.3 MB)
This file contains Supplementary Table 13.10.
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