Assessing de novo parasite genomes assembled using only Oxford Nanopore Technologies MinION data.

In this study, we assessed the quality of de novo genome assemblies for three species of parasitic nematodes (Brugia malayi, Trichuris trichiura, and Ancylostoma caninum) generated using only Oxford Nanopore Technologies MinION data. Assemblies were compared to current reference genomes and against additional assemblies that were supplemented with short-read Illumina data through polishing or hybrid assembly approaches. For each species, assemblies generated using only MinION data had similar or superior measures of contiguity, completeness, and gene content. In terms of gene composition, depending on the species, between 88.9 and 97.6% of complete coding sequences predicted in MinION data only assemblies were identical to those predicted in assemblies polished with Illumina data. Polishing MinION data only assemblies with Illumina data therefore improved gene-level accuracy to a degree. Furthermore, modified DNA extraction and library preparation protocols produced sufficient genomic DNA from B. malayi and T. trichiura to generate de novo assemblies from individual specimens.

DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus.

BACKGROUND: The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes. RESULTS: We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies/µL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments. CONCLUSIONS: DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.

First Insights into Population Structure and Genetic Diversity Versus Host Specificity in Trypanorhynch Tapeworms Using Multiplexed Shotgun Genotyping.

Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) data sets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted Rhinoptericola megacantha (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of R. megacantha are more host-specific and less broadly distributed than adults of C. gracilis, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For R. megacantha, population structure coincided with geography rather than host species. For C. gracilis, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.

Novelty and phylogenetic affinities of a new family of tapeworms (Cestoda: Rhinebothriidea) from endangered sawfish and guitarfish.

The parasites of hosts of conservation concern are often poorly known. This is the case with the iconic group of elasmobranchs known as the sawfish of the genus Pristis, all four species of which are considered as Endangered or Critically Endangered by the International Union for Conservation of Nature (IUCN, Switzerland). Examination of cestodes from three species of sawfish (Pristis pristis, Pristis clavata, and Pristis zijsron) in Australia and one of their close relatives, the also critically endangered widenose guitarfish, Glaucostegus obtusus, in India, collected over the past 25 years, yielded four new species of tapeworms which are described herein. All four belong to the previously monotypic Mixobothrium; the diagnosis of the genus is revised to accommodate the new species. Among the new taxa is a species that had been included in previous molecular phylogenies but whose identity and affinities within the order Rhinebothriidea, and thus also its familial placement, were unclear. This species exhibits the morphological features of Mixobothrium and thus its identity is, at long last, revealed. Sequence data generated for the 28S rDNA gene for three of the new species, as well as an additional new but yet undescribed species from Pristis pectinata from Florida (USA), confirms the uniqueness of this group among the rhinebothriideans. The new family Mixobothriidae is established to house these taxa. The members of this family differ from all but one of the five other families of rhinebothriideans in lacking apical suckers on their bothridia. They are also distinctive in that their bothridia are divided into three regions. The anterior and posterior regions have similar locular configurations to one another and differ from the locular configuration of the middle region. As a consequence, the bothridia are symmetrical along both their vertical and horizontal axes. We predict that a focus on species of guitarfish in the genus Glaucostegus will be the most productive approach for discovering additional diversity in this family of cestodes.

A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida).

Since 2010, the trypanorhynch tapeworm family Rhinoptericolidae Carvajal & Campbell, 1975 has housed just two distinctive, monotypic genera (Rhinoptericola Carvajal & Campbell, 1975 and Nataliella Palm, 2010). However, global collections of tapeworms from sharks and rays over the last more than three decades brought to light the need for major revision of the family by suggesting a much greater species-level diversity for the nominal genus Rhinoptericola. Through synonymy and the description of new species, the number of species in the genus is increased from one to eight. A phylogenetic analysis of the D1-D3 gene region of 28S rRNA (28S), including seven of the now nine species of rhinoptericolids, and a broad sampling of the other Trypanobatoida is the first to recover a monophyletic Rhinoptericolidae. In addition to systematic revision, this study allowed for the first evaluation of the degree of intraspecific vs interspecific variation in 28S for adult trypanorhynchs across the various hosts and geographic localities from which they have been reported, suggesting a relatively consistent boundary for Rhinoptericola. It is further suggested that detailed scanning electron microscopy (SEM) images of both the basal and metabasal armatures greatly aid in the interpretation of hook arrangement and shape. A schematic to streamline determination of the tentacular surface presented in scanning electron micrographs and line drawings of trypanorhynchs is presented for species with both two and four bothria. In combination, these methodological refinements can now be used as a model to resolve issues of classification and non-monophyly within both major lineages of the Trypanorhyncha. As a result of the taxonomic work, Rhinoptericola megacantha Carvajal & Campbell, 1975 (previously only known from the American cownose ray from the Chesapeake Bay and the Ticon cownose ray from the Gulf of Mexico, Venezuela, and Brazil) is now known from an additional species of cownose ray and a species of stingray, and is revealed to have a transatlantic distribution. Data from SEM suggest a simpler interpretation of hook arrangement in the metabasal armature for Rhinoptercola and-in combination with 28S sequence data-support Shirleyrhynchus Beveridge & Campbell, 1988 (a former rhinoptericolid) as its junior synonym. The three species formerly assigned to Shirleyrhynchus are thus transferred to Rhinoptericola. Data from light microscopy on whole-mounted specimens and histological sections, SEM, and 28S showed the eutetrarhynchid Prochristianella jensenae Schaeffner & Beveridge, 2012b to be morphologically consistent with species of Rhinoptericola and it is thus transferred to the genus. The type series of P. jensenae was determined to be mixed, representing two distinct species which are here redescribed and described as new, respectively. Two additional novel species of Rhinoptericola are described from cownose rays from off Mozambique and the Gulf of California.

Five New Species of the Tapeworm Genus Anthocephalum (Rhinebothriidea: Anthocephaliidae) Parasitizing A Single Species of Indo-Pacific Stingray and A Revised Diagnosis of the Genus.

Five new species of the elasmobranch tapeworm genus Anthocephalum Linton, 1890 (Rhinebothriidea: Anthocephaliidae Ruhnke, Caira and Cox, 2015 ) are described from the mangrove whipray, Urogymnus granulatus (Macleay) from the Solomon Islands and northern Australia. Anthocephalum blairi n. sp., Anthocephalum gravisi n. sp., Anthocephalum haroldsoni n. sp., Anthocephalum mounseyi n. sp., and Anthocephalum ruhnkei n. sp. differ from one another and their congeners based on quantitative and qualitative features of the scolex and proglottid anatomy. Species boundaries recognized by these distinguishing morphological features are supported by a maximum likelihood phylogenetic analysis based on combined 18S rDNA and 28S rDNA (D1-D3) sequence data showing the new species as independent lineages among 13 of the 18 species of Anthocephalum described to date. Several morphological features (the possession of columns of vitelline follicles that are interrupted by the ovary, a uterus that does not extend to the anterior margin of the proglottid but stops short in the anterior region of the field of testes, proximal surfaces of the marginal loculi covered with acicular filitriches only throughout, or with gladiate spinitriches and acicular filitriches throughout, and proximal bothridial surfaces with gladiate spinitriches and acicular filitriches) are collectively exhibited by the 5 new species and have not been documented previously in other species of Anthocephalum. The genus is herein amended to reflect these features. Additionally, the replacement name Anthocephalum centrurum ( Southwell, 1925 ) Ruhnke, 1994 is reinstated as the valid name for the type species of the genus, Anthocephalum gracile Linton, 1890 , with the latter being the junior secondary homonym of A. gracile ( Wedl, 1855 ) Ruhnke, 1994 . The description of these new species increases the number of valid species of Anthocephalum from 18 to 23.

A new genus with two new species of lecanicephalidean tapeworms (Cestoda) from the mangrove whipray, Urogymnus granulatus (Myliobatiformes: Dasyatidae),from the Solomon Islands and northern Australia.

A new lecanicephalidean genus is erected for cestodes previously recognised as "New Genus 12" (Polypocephalidae) in a phylogenetic analysis of the interrelationship of members of this order. Examination of the cestode fauna of the mangrove whipray, Urogymnus granulatus (Macleay) (Myliobatiformes: Dasyatidae) from the Solomon Islands and northern Australia revealed the existence of specimens representing two new species, consistent in morphology with "New Genus 12." Corollapex gen. n. is unique among the 24 valid lecanicephalidean genera in its possession of an apical organ in the form of an external retractable central disk surrounded by eight concave muscular, membrane-bound pads and an internal heterogeneous glandular component. The two new species described herein, Corollapex cairae sp. n. (type species) and Corollapex tingoi sp. n., differ from one another in overall size and number of mature and immature proglottids, and are noted to demonstrate a differential distribution between mature and juvenile host individuals. Additional species diversity in the new genus, beyond C. cairae sp. n., C. tingoi sp. n., and "New Genus 12 n. sp. 1" of Jensen et al. (2016) is suggested. Corollapex gen. n. appears to be restricted to dasyatid hosts in the Indo-West Pacific region.

A new genus of rhinebothriidean cestodes from batoid elasmobranchs, with the description of five new species and two new combinations.

Survey work of batoid elasmobranchs in the eastern Atlantic and Indo-Pacific revealed multiple species of a new genus of cestode. Stillabothrium Healy et Reyda gen. n. (Rhinebothriidea: Escherbothriidae) is unique in its possession of an even number of non-medial longitudinal septa in the posterior portion of the bothridia, resulting in a series of loculi that are longer than wide (i.e. vertically oriented) and are arranged in columns. Five new species of Stillabothrium are described, S. ashleyae Willsey et Reyda sp. n., S. davidcynthiaorum Daigler et Reyda sp. n., S. campbelli Delgado, Dedrick et Reyda sp. n., S. hyphantoseptum Herzog, Bergman et Reyda sp. n., S. jeanfortiae Forti, Aprill et Reyda sp. n., and two species are formally transferred to the genus, S. amuletum (Butler, 1987) comb. n., and S. cadenati (Euzet, 1954) comb. n., the latter of which is redescribed. The species differ in the configuration of the other bothridial septa and in proglottid anatomy. Species of Stillabothrium were found parasitising a total of 17 species of batoid elasmobranchs of the genera Dasyatis Rafinesque, Glaucostegus Bonaparte, Himantura Müller et Henle, Pastinachus Rüppell, Rhinobatos Linck and Zanobatus Garman, including several host species that are likely new to science. A phylogenetic hypothesis based on Bayesian analysis of 1 084 aligned positions of the D1-D3 region of 28S rDNA for 27 specimens representing 10 species of Stillabothrium and two outgroup species supported the monophyly of Stillabothrium. These results also supported morphologically determined species boundaries in all cases in which more than one specimen of a putative species was included in the analysis. Host specificity appears to vary across species of Stillabothrium, with the number of host species parasitised by each species of Stillabothrium ranging from one to four. The geographic distribution of species of Stillabothrium spans the eastern Hemisphere, including the eastern Atlantic (coastal Senegal) and several locations in the Indo-Pacific (coastal Vietnam, Borneo and Australia). In addition, Phyllobothrium biacetabulatum Yamaguti, 1960 is formally transferred into family Escherbothriidae, although its generic placement remains uncertain (species incertae sedis).