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Gyrocotyle discoveryi n. sp. Type-host: Hydrolagus mirabilis (Collett) (Chimaeriformes: Chimaeridae), large-eyed rabbitfish. Type-locality: Goban Spur, North-East Atlantic. Other localities: Porcupine Seabight (51��09 0 N, 11��55 0 W, depth 1,200 m, 30.xi.2002, RRS Discovery Cruise, No. 15048-14, 15); Goban Spur (49��49 0 N, 11��44 0 W, depth 1,175���1,250 m, 27.iv.2001, RRS Discovery Cruise 252, No. 13963/17, 20, 24, 72; 49��41 0 N, 11��53 0 W, depth 1,053���1,077 m, 23.iv.2001, RRS Discovery Cruise 252, No. 13962/4; 49��47 0 N, 11��58 0 W, depth 1,240���1,360 m, 19.x.2002, RRS Discovery Cruise D 266, No. 15066-124, 125; 51��09 0 N, 11��55 0 W, depth 1200 m, 30.ix.2002, RRS Discovery Cruise D 266, No. 15063-103), North-East Atlantic. Type-material: Holotype (NHMUK 2019.11.21.3), paratypes (NHMUK.2019.11.21.4-13 from Goban Spur; NHMUK.2019.11.21.14-19 from Porcupine Sea Bight).). Site in host: Spiral intestine. Representative DNA sequences: MN655879 and MN655881 (ssrDNA); MN657003-MN657005, MN657007- MN657009, MN657011 (lsrDNA, domains D1-D3). ZooBank registration: The Life Science Identifier (LSID) for Gyrocotyle discoveryi n. sp. is urn:lsid:- zoobank.org:act:7B028A0B-B8EB-495E-A9F1- F29DDB60B89A. Etymology: The species is named after the RRS Discovery, the NERC research vessel on which the specimens were collected. Description [Based on 17 specimens; Figs. 4���6.] With characters of the order. Body relatively squat, with deeply crenulated margins, 8,634 ���17,586 X 4,996 ���8,439 (12,071 X 6,676), width 36���98 (60)% of length. Anterior sucker distinct, 1,149 ���1,621 (1,347) long, 596���1,022 (771) wide. Uterus large, in central part of body, 1,546 ���2,996 (2,232) from anterior extremity, 2,453 ���6,226 (4,533) long, 35���43 (38)% of body length. Rosette distinct, fairly complex, 1,797 ���3,092 (2,575) long, junction with soma not clear. Eggs tanned, operculate, 85��� 97 X 39���56 (89 X 49). Diagnosis Gyrocotyle discoveryi n. sp. can be diagnosed from other congeners on the basis of unique nucleotide characters in our rDNA alignments (listed as alignment position-nucleotide): ssrDNA: 176-G, 782-G, 862-G, 973-C; lsrDNA: 573-A, 800-T, 1,245-C, 1,246- C, 1,247-G, 1,360-T, 1,369-T, 1,375-C, 1,379-G, 1,382-G, 1,391-A, 1,449-T, 1,468-T, 1,477-T. Remarks Mauchline & Gordon (1984) reported a ������cestode������ in Hy. mirabilis from the Rockall Trough off NW Scotland, which is, as far as we are aware, the only possible record of a Gyrocotyle from this host. Two species of Gyrocotyle, G. major van der Land & Templeman, 1968 and G. abyssicola van der Land & Templeman, 1968, have been reported from its congener, the small-eyed rabbit fish Hydrolagus affinis (de Brito Capello) on the edges of the continental shelf off the eastern coast of Newfoundland (van der Land & Templeman, 1968). These two species are illustrated as much more elongate than our specimens, with less complex lateral wrinkling and small rosettes. The worms were recovered from frozen hosts, so the gross morphology may well not be of significance in differentiating these species. Subsequently, these two taxa have been reported from the same host species off south-western Greenland by Karlsbakk et al. (2002) and, puzzlingly, from a rhinochimaerine species, the straight-nosed rabbit fish Rhinochimaera atlantica Holt & Byrne, off the Scotian Shelf by Hogans & Hurlbut (1984). In the North-East Atlantic, R. atlantica has not been found harbouring Gyrocotyle, but it does harbour the strobilate tapeworm Chimaerocestos prudhoei Williams & Bray, 1984 and a congeneric host, the Pacific spookfish R. pacifica (Mitsukuri, 1895) also harbours a species of Chimaerocestos Williams & Bray, 1984 (see Caira et al., 1999, 2014). Other records of Gyrocotyle spp. from Hydrolagus spp. are from the Pacific Ocean (see Bandoni & Brooks, 1987). There are no reliable morphological characters to differentiate this species or indeed any of the gyrocotylidean species circumscribed by molecular means. Therefore, the species is diagnosed by its relatively marked sequence divergence from those of recognised species., Published as part of Bray, Rodney A., Waeschenbach, Andrea, Littlewood, D. Timothy J., Halvorsen, Odd & Olson, Peter D., 2020, Molecular circumscription of new species of Gyrocotyle Diesing, 1850 (Cestoda) from deep-sea chimaeriform holocephalans in the North Atlantic, pp. 285-296 in Systematic Parasitology 97 on pages 292-293, DOI: 10.1007/s11230-020-09912-w, http://zenodo.org/record/4623814, {"references":["Mauchline, J., & Gordon, J. D. M. (1984). Incidence of parasitic worms in stomachs of pelagic and demersal fish of the Rockall Trough, northeastern Atlantic Ocean. Journal of Fish Biology, 24, 281 - 285.","van der Land, J., & Templeman, W. (1968). Two new species of Gyrocotyle (Monogenea) from Hydrolagus affinis (Brito Capello) (Holocephali). Journal of the Fisheries Research Board of Canada, 11, 2365 - 2385.","Karlsbakk, E., Aspholm, P. E., Berg, V., Hareide, N. R., & Berland, B. (2002). Some parasites of the small-eyed rabbitfish, Hydrolagus affinis (Capello, 1867) (Holocephali), caught in deep waters off SW Greenland. Sarsia, 87, 179 - 184.","Hogans, W. E., & Hurlbut, T. R. (1984). Parasites of the knifenose chimaera, Rhinochimaera atlantica, from the northwest Atlantic Ocean. Canadian Field-Naturalist, 98, 365.","Williams, H. H., & Bray, R. A. (1984). Chimaerocestos prudhoei gen. et sp. nov., representing a new family of tetraphyllideans and the first record of strobilate tapeworms from a holocephalan. Parasitology, 88, 105 - 116.","Caira, J. N., Jensen, K., & Healy, C. J. (1999). On the phylogenetic relationships among tetraphyllidean, lecanicephalidean and diphyllidean tapeworm genera. Systematic Parasitology, 42, 77 - 151.","Caira, J. N., Jensen, K., Waeschenbach, A., Olson, P. D., & Littlewood, D. T. J. (2014). Orders out of chaos - molecular phylogenetics reveals the complexity of shark and stingray tapeworm relationships. International Journal for Parasitology, 44, 55 - 73.","Bandoni, S. M., & Brooks, D. R. (1987). Revision and phylogenetic analysis of the Gyrocotylidea Poche, 1926 (Platyhelminthes: Cercomeria: Cercomeromorpha). Canadian Journal of Zoology, 65, 2369 - 2389."]}

Gyrocotyle haffii n. sp. Type-host: Harriotta raleighana Goode & Bean (Chimaeriformes: Rhinochimaeridae), bent-nosed chimaera. Type-locality: Goban Spur (49°46 0 N, 12°21 0 W, depth 1,631–1,653 m, 22-23.iv.2001; RRS Discovery Cruise 252, No. 13951/14), North-East Atlantic. Type-material: Holotype (NHMUK. 2019.11.21.1), paratype (NHMUK. 2019.11.21.2). Site in host: Spiral intestine. Representative DNA sequences: MN655880 (ssrDNA); MN657006 (lsrDNA, domains D1-D3). ZooBank registration: The Life Science Identifier (LSID) for Gyrocotyle haffii n. sp. is urn:lsid:- zoobank.org:act:7717F9D6-4C9D-4C59-8D0A- 4C5E306B4671. Etymology: The species is named in honour of our late colleague and friend Professor Harford ‘Haffi 0 Williams in recognition of his contribution to the understanding of the Gyrocotylidea. Description [Based on a single intact, immature whole worm and second immature worm from which the central portion had been excised for molecular analysis; Figs. 2, 3]. With characters of the order. Body elongate with minute annular ridges; no large lateral flap. Length 23,504; greatest width near anterior extremity, 3,131. Rosette relatively small with few crenulations, 1,943 long. Anterior sucker large, oval, 1,750 X 1,223. Reproductive system immature; anlagen commences 2,852 from anterior extremity, 8,191 long; consisting of a long, narrow patch of stained tissue reaching, and a branched section passing, towards lateral margin of worm; apparently opening at c. 268 from anterior extremity. Only other evidence of reproductive organs is putative vitelline glands scattered around posterior extremity of anlagen. Diagnosis Gyrocotyle haffii n. sp. can be diagnosed from other congeners on the basis of unique nucleotide characters in our rDNA alignments (listed as alignment positionnucleotide): ssrDNA: 218-T, 723-A, 746-C, 747-A, 748-G, 1,158-T, 1,654-G, 1,673-C, 2,115-C; lsrDNA: 612-T, 837-A, 875-T, 1,306-A, 1,395-C, 1,402-A, 1,501-G. Remarks As far as we are aware there is only one previous report of a gyrocotylidean from Ha. raleighana, the bentnose chimaera. Parukhin (1966) reported ‘‘ Gyrocotyloides nybelini Fuhrmann, 1931 ’’ in this host from the South Atlantic Ocean. Parukhin (1968) repeated this report saying (in translation) ‘‘Found in Callorhynchus capensis. Two adult parasites were found in two fish. In addition, six larvae were found in one of them. In addition to C. capensis, specimens were found in two Hariota [sic] raleighana. In both cases there were two specimens. Previously, this species was observed in the Atlantic in Chimaera monstrosa ’’. In addition, it seems likely that the records of ‘cestode adults 0 from Ha. raleighana, Hy. mirabilis and C. monstrosa from the Rockall Trough off NW Scotland by Mauchline & Gordon (1984) refer to Gyrocotyle spp. There is no reliable morphological character to differentiate this species or indeed any of the gyrocotylidean species circumscribed by molecular means. Therefore, the species is diagnosed by its relatively marked sequence divergence from those of recognised species.

Additional file 9: Figure S7. Alignment of the N-terminal regions encoded by a tandem array of micro-exons genes located on Chr 6. The shared amino acid motif (consensus MRLFILLCFAVTLWAC) indicates that this gene array evolved through tandem duplication.

Additional file 7: Figure S5. Optical map contigs aligned to the genome assembly of the rRNA repeat array. Five contigs from the optical map are shown with the segment that aligns to the sequenced repeat indicated by coloured bars. The largest map contig (arrow) represents one haplotype containing the rRNA tandem repeat (pink bar) as well as the left (blue bar) and right (yellow bar) flanking regions. Other optical map contigs either contain the repeat together with either 5’ or 3’ flanking region, and likely represent an alternative haplotype, or have an insufficient amount of unique sequence to unambiguously determine their position within the repeat array.

Additional file 8: Figure S6. Whole genome optical maps aligned to v3 assembly. Circled regions show where optical map data indicate alternative haplotypic versions. Regions labelled A and B, together with the rRNA array, represent the largest repeat regions where haplotype differences could account for visible length differences in sister chromatids (see text). Chromosomes are numbered and the positions of the telomeric repeats indicated by red dots.

Additional file 12: Figure S10. The terminal centromeric repeat of chromosome 2. A dotter plot shows that the centromeric repeat not only contains a second dominant repeat motif but is also interspersed with other repetitive elements, unlike the other chromosomes that exhibit a tandem array comprised entirely of the novel 179mer. Within the interstitial sequences we find the top blastx hit to Gag-Pol polyprotein, indicating the centromere has been invaded by transposable elements.

Additional file 3: Figure S1. Mitochondrial genome. The 13,919 bp Hymenolepis microstoma mitochondrial genome was re-assembled from both short and long-read data, yielding over 1000x coverage. The new assembly resolved the full length of a region involving a tandemly repeated 32 bp motif (cf. GenBank accession AP017665.1). This region is identified as one of three origins of replication-heavy strand (OH-a) by MITOS [61] and an adjacent hairpin-loop region as the origin of replication-light strand (OL). Gene order of ribosomal and protein-coding genes is consistent with the hypothesized ground-plan for the mitogenomes of parasitic flatworms as is the absence of the atp8 gene [89].

Additional file 1 Tables S1-S5: Table S1 Network clustering. The proteins of the top ten clusters with in-cluster degree and MCODE protein score. Hub proteins (main text Table 2 are denoted *). Table S2 Differential expression. The 176 differentially-expressed genes identified between adults and 5-day old, metamorphosing larvae that form a sub-network of 668 interactions (main text Fig. 8). Table S3 Low throughput data. The low throughput (=200 interactions). Interaction data were limited to physical interactions (Ints) from eukaryotic species then split into individual datasets by species and by study based on PubMed ID (PMID). Table S5 Genes of interest. The protein components of signalling pathways, transcription factors and ‘multipotency’ germline/stem-cell-related genes used to extract subnetworks in main text section Specific genes of interest: signalling, transcription and germline-related genes.

Additional file 6: Figure S4. Comparison of RNA-seq sample counts against the v2 and v3 assemblies and gene models. Principle component analyses (A) show tight clustering of sample replicates based on counts using both assemblies, while in the v3 (right) the Larvae, Scolex-Neck and Whole Adult samples are arrayed only along PC1, with the transcriptome of the Scolex-Neck mid-way between those of the Larvae and Whole Adult samples. The Mid and End samples are further differentiated from the other samples along PC2. Heatmap clustering (B) shows that the transcriptome of the Scolex-Neck region is more similar to that of mid-metamorphose larvae than to middle or end regions of the adult worm, as discussed in [8].

Background Early developmental patterns of flatworms are extremely diverse and difficult to compare between distant groups. In parasitic flatworms, such as tapeworms, this is confounded by highly derived life cycles involving indirect development, and even the true orientation of the tapeworm antero-posterior (AP) axis has been a matter of controversy. In planarians, and metazoans generally, the AP axis is specified by the canonical Wnt pathway, and we hypothesized that it could also underpin axial formation during larval metamorphosis in tapeworms. Results By comparative gene expression analysis of Wnt components and conserved AP markers in the tapeworms Echinococcus multilocularis and Hymenolepis microstoma, we found remarkable similarities between the early stages of larval metamorphosis in tapeworms and late embryonic and adult development in planarians. We demonstrate posterior expression of specific Wnt factors during larval metamorphosis and show that scolex formation is preceded by localized expression of Wnt inhibitors. In the highly derived larval form of E. multilocularis, which proliferates asexually within the mammalian host, we found ubiquitous expression of posterior Wnt factors combined with localized expression of Wnt inhibitors that correlates with the asexual budding of scoleces. As in planarians, muscle cells are shown to be a source of secreted Wnt ligands, providing an explanation for the retention of a muscle layer in the immotile E. multilocularis larva. Conclusions The strong conservation of gene expression between larval metamorphosis in tapeworms and late embryonic development in planarians suggests, for the first time, a homologous developmental period across this diverse phylum. We postulate these to represent the phylotypic stages of these flatworm groups. Our results support the classical notion that the scolex is the true anterior end of tapeworms. Furthermore, the up-regulation of Wnt inhibitors during the specification of multiple anterior poles suggests a mechanism for the unique asexual reproduction of E. multilocularis larvae. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0233-x) contains supplementary material, which is available to authorized users.