A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites

Revision of the 'Acanthephyra purpurea' species complex (Crustacea: Decapoda), with an emphasis on species diversification in the Atlantic

We inventoried all nine species of the 'Acanthephyra purpurea' complex, one of the most abundant and cosmopolitan group of mesopelagic shrimps. We used 119 specimens at hand and genetic data for 124 specimens from GenBank and BOLD. Phylogenetic analysis of four genes (COI, 16S, NaK, and enolase) showed that the 'Acanthephyra purpurea' complex is polyphyletic and encompasses two species groups, 'A. purpurea' (mostly Atlantic) and 'A. smithi' (Indo-West Pacific). The 'A. purpurea' species group consists of two major molecular clades A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa. Molecular data suggest that hitherto accepted species A. acanthitelsonis, A. pelagica, and A. sica should be considered as synonyms. The Atlantic is inhabited by at least two cryptic genetic lineages of A. pelagica and A. quadrispinosa. Morphological analyses of qualitative and quantitative (900 measurements) characters resulted in a tabular key to species and in a finding of four evolutionary traits. Atlantic species showed various scenarios of diversification visible on mitochondrial gene level, nuclear gene level, and morphological level. We recorded and discussed similar phylogeographic trends in diversification and in distribution of genetic lineages within two different clades: A. pelagica and A. kingsleyi - A. purpurea - A. quadrispinosa.

Metarhabditis amsactae: A potential biopesticide isolated from Punjab (India) with potent insecticidal activity and immunomodulatory effects against Galleria mellonella (Lepidoptera: Pyralidae)

A survey was undertaken to isolate entomopathogenic nematodes from Amritsar district of Punjab, India. Out of 20 soil samples collected, two were found positive for the presence of nematodes. 18S and ITS rDNA gene sequencing revealed their identity as Metarhabditis amsactae. To assess its biocontrol potential, Galleria mellonella larvae were treated with concentrations of 20, 40, 80 and 160 IJs/L (infective juveniles/larva) and mortality was recorded from 24 h up to 96 h of nematode exposure. Distilled water without nematodes was used as an untreated control. M. amsactae showed potent larvicidal activity against G. mellonella that was found to be concentration and time dependent. Nematode infection caused 93.33 % larval mortality at 80 IJs/L after 72 h of treatment. 100 % mortality was observed after 96 h. No mortality was observed in control. To evaluate the immunomodulatory effects of M. amsactae, G. mellonella larvae were infected with 100 IJs/L and activities of antioxidant and detoxifying enzymes viz., superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APOX), phenol oxidase (PO), glutathione-S-transferase (GST) and acetylcholine esterase (AChE) were appraised after 12, 24, 36 and 48 h of nematode exposure. Malondialdehyde content was also determined. The results obtained demonstrated a significant elevation in all the enzyme activities at all time intervals in treated larvae when compared with untreated control. MDA levels were also enhanced in response to nematode infection. Thus, the present study revealed high insecticidal potential and immunomodulatory effects of M. amsactae on G. mellonella that should be further explored on other insect pests as well.

Detection and Analysis of Wolbachia in Plant-Parasitic Nematodes and Insights into Wolbachia Evolution

Since the discovery of Wolbachia in plant-parasitic nematodes (PPNs), there has been increased interest in this earliest branching clade that may hold important clues to early transitions in Wolbachia function in the Ecdysozoa. However, due to the specialized skills and equipment of nematology and the difficulty in culturing most PPNs, these PPN-type Wolbachia remain undersampled and poorly understood. To date, there are few established laboratory methods for working with PPN-type Wolbachia strains, and most research has relied on chance discovery and comparative genomics. Here, we address this challenge by providing detailed methods to assist researchers with more efficiently collecting PPNs and screen these communities, populations, or single nematodes with a newly developed PPN-type Wolbachia-specific PCR assay. We provide an overview of the typical yields and outcomes of these methods, to facilitate further targeted cultivation or experimental methods, and finally we provide a short introduction to some of the specific challenges and solutions in following through with comparative or population genomics on PPN-type Wolbachia strains.

A new species of Rhyncholagena Lang, 1944 (Copepoda, Harpacticoida, Miraciidae) from Palau

A new species of Miraciidae Dana, 1846, Rhyncholagenacuspissp. nov., was described from Palau. Morphological descriptions and gene fragment sequence barcoding were performed on the 11th species of Rhyncholagena Lang, 1944 collected from sandy sediment samples in the subtidal zone of the Philippine Sea, Palau. Morphological characteristics were compared and an updated identification key was provided. A new species, Rhyncholagenacuspissp. nov., was found to be morphologically similar to Rhyncholagenalittoralis Por, 1967 and R.bermudensis Malt, 1990. This is the first record of the genus Rhyncholagena in Palau. The study provides basic data for future studies and highlights the need for continued exploration of marine biodiversity in Palau and other regions.

FLInt: single shot safe harbor transgene integration via Fluorescent Landmark Interference

The stable incorporation of transgenes and recombinant DNA material into the host genome is a bottleneck in many bioengineering applications. Due to the low efficiency, identifying the transgenic animals is often a needle in the haystack. Thus, optimal conditions require efficient screening procedures, but also known and safe landing sites that do not interfere with host expression, low input material and strong expression from the new locus. Here, we leverage an existing library of ≈300 different loci coding for fluorescent markers that are distributed over all 6 chromosomes in Caenorhabditis elegans as safe harbors for versatile transgene integration sites using CRISPR/Cas9. We demonstrated that a single crRNA was sufficient for cleavage of the target region and integration of the transgene of interest, which can be easily followed by loss of the fluorescent marker. The same loci can also be used for extrachromosomal landing sites and as co-CRISPR markers without affecting body morphology or animal behavior. Thus, our method overcomes the uncertainty of transgene location during random mutagenesis, facilitates easy screening through fluorescence interference and can be used as co-CRISPR markers without further influence in phenotypes.

Diversification of the shell shape and size in Baikal Candonidae ostracods inferred from molecular phylogeny

Ostracod shells are used extensively in paleontology, but we know little about their evolution, especially in ancient lakes. Lake Baikal (LB) is the world's most important stronghold of Candonidae diversity. These crustaceans radiated here rapidly (12-5 Ma) and with an unprecedented morphological diversity. We reconstruct their molecular phylogeny with 46 species and two markers (18S and 16S rRNA), and use it to estimate the evolution of the shell shape and size with landmark-based geometric morphometrics (LBGM). High posterior probabilities support four major clades, which differ in node depth and morphospace clustering. After removing a significant allometry, the first three principal components (PCs) describe about 88% of total variability, suggesting a strong integration. Reconstructed ancestral shapes are similar for all four clades, indicating that diversification happened after colonization. Major evolutionary changes occurred from trapezoidal to elongated shapes. Sister species are separated in morphospace, by centroid size, or both, as well as by vertical and horizontal distributions in LB. Ostracod shell is a strongly integrated structure that exhibits high evolvability, with some extreme shapes, although mostly along the first PC. This is the first study that combines molecular phylogeny and LBGM for ostracods and for any LB group.

Characterization of a Root-Knot Nematode Infecting Aconitum carmichaelii in Southwest China

Growth of the Chinese herbal medicine industry has resulted in several new pests and diseases. China is one of the world largest producers of monkshood (Aconitum carmichaelii Debx.), but an unidentified root-knot nematode has become a significant pest in the southwestern provinces of Yunnan and Sichuan. Morphological characteristics and the ribosomal DNA-internal transcribed spacer and D2-D3 region of the 28S ribosomal RNA gene sequences were used to identify the nematode as Meloidogyne hapla. Through investigation, this is the first report of M. hapla infecting monkshood in Yunnan and Sichuan Provinces.

A new isolate of Mesorhabditis monhystera (Bütschli, 1873) Dougherty, 1955 (Rhabditida: Rhabditidae): re-evaluated with molecular data and scanning electron microscopic observations

A new isolate of Mesorhabditis monhystera (Bütschli, ) Dougherty, is described and illustrated with morphological and molecular data. The phylogenetic analysis based on the D2/D3 segment of 28S rDNA using the Bayesian inference method, revealed monophyly of the genus Mesorhabditis as the subordinate taxa clustered in one clade. The clade further divided into two subclades representing the Monhystera-group and Spiculigera-group with 100% posterior probability values. However, GenBank sequences of several species constituting the Monhystera-group, showed high similarity and very little genetic divergence (98-99%) of up to 4-5 bases. In order to ascertain the status of those isolates, detailed morphological comparison is provided along with a pictorial key. A sequence-based phylogeography of haplogroups of Mesorhabditis using the median-joining network method, was also inferred. The results suggested the need for morphological validation of a species before its sequences are deposited in GenBank.

A New Species of the Genus Robertgurneya Apostolov & Marinov, 1988 (Copepoda: Harpacticoida: Miraciidae) from a Sublittoral Zone of Jeju Island, Korea

A new species, Robertgurneya jejuensis sp. nov., was described from sandy sediment samples collected at a depth of 25 m on Mun Island, Jeju, in June 2018. The new species is morphologically similar to Robertgurneya similis similis (Scott A., 1896) and Robertgurneya donghaensis Bang, 2021; this is the second record of the genus Robertgurneya in South Korea. The morphological characteristics of the similis group within the genus Robertgurneya, to which the new species is ascribed, are summarized here. Furthermore, an identification key is provided based on the summary. Molecular identification of the collected specimens, based on the nuclear 18S ribosomal RNA (18S rRNA) and the mitochondrial cytochrome oxidase subunit I fragment, was obtained. Finally, a phylogenetic tree was constructed to present the position of Robertgurneya within the Miraciidae family based on 18S rRNA sequences which is relatively conserved. As a result, the relationship with sister genera morphologically similar to Robertgurneya was also molecularly confirmed.

Ficophagus giblindavisi n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus variegata in China

A new species of the genus Ficophagus was recovered from the syconia of Ficus variegata from Shenzhen, Guangdong province, China. It is described herein as Ficophagus giblindavisi n. sp. and is characterised by possessing the longest stylet in males (35.1-45.8 μm) and most lateral incisures (5) of all currently described species in the genus, a short PUS (8.4-11.4 μm or 0.3 VBD long), excretory pore situated at or posterior to the nerve ring, amoeboid sperm, three pairs of subventral papillae on the male tail, rounded male tail tip with a mucron, absence of gubernaculum and sickle-shaped spicules with a terminal cucullus. Ficophagus giblindavisi n. sp. was differentiated from other sequenced species by the partial small subunit (SSU) rRNA gene and D2-D3 expansion segments of the large subunit (LSU) rRNA gene. Phylogenetic analysis with the LSU D2-D3 expansion segment sequence suggested that F. giblindavisi n. sp. is clustered in the same highly supported monophyletic clade with F. auriculatae and F. fleckeri.

Molecular and phenotypic characterization of two cryptic species of the predatory genus Mononchoides Rahm, 1928 (Rhabditida: Diplogastridae) and their congeneric affinities

Based on morphometric, morphological and molecular characterization using partial small subunit 18S ribosomal DNA (rDNA) and the D2/D3 domain of large subunit 28S rDNA, we described a new species Mononchoides kanzakii collected from manure, and the known species Mononchoides composticola Steel, Moens, Scholaert, Boshoff, Houthoofd and Bert, 2011, isolated from the dung beetle Oniticellus cinctus (Fabricius, 1775). Phylogenetic trees based on the evolutionary model (GTR + I + G) were inferred by Bayesian inference algorithms. Mononchoides kanzakii sp. n. is characterized by 28-32 longitudinal ridges, discontinuous at level of stoma; amphidial apertures inconspicuous; metastegostom armed with thorn-shaped dorsal tooth; a flattened, claw-like right subventral tooth, and left subventral denticulate ridge with 12-14 fine denticles delimited by a group of five denticles in females vs. triangular, flattened right subventral tooth, 5-8 prominent denticles at left subventral sector in males; cloacal lips with a distinct rim; and gubernaculum with cuticularized, proximal and distal extensions of equal length, each constituting half of the length of the wider part of gubernaculum.

Four new Parasterope (Ostracoda, Myodocopina) from the Northwest Pacific and their phylogeny based on 16S rRNA

Parasterope Kornicker, 1975 is a marine ostracod genus with 49 species described so far, which makes it the most diverse representative of the subfamily Cylindroleberidinae, as well as the entire family Cylindroleberididae. Despite its global distribution no species are reported from South Korea. Three new species collected from the Korean coast of the Sea of Japan (Parasteropebusanensissp. nov., P.singulasp. nov., and P.sohisp. nov.), and one from the Japanese coast of the Pacific Ocean (P.sagamisp. nov.) are described. A taxonomic key to all named species from East Asia is provided. A phylogenetic tree is reconstructed based on partial 16S rRNA sequences of the four new species and other Cylindroleberidinae available from GenBank. Monophyly of Parasterope is supported by high posterior probabilities, but the phylogenetic analyses also indicate that some of the GenBank data attributed to this genus are probably misidentifications. A map of distribution and a checklist of all described Parasterope species are also provided.

Description of Laimaphelenchus piceae sp. n., a new evidence of cryptic speciation, and L. sinensis Gu et al., 2020 (Rhabditida: Aphelenchoididae), a record from Shanxi province, north China

This contribution deals with the record and description of one new species and record of one known species of the genus Laimaphelenchus from Shanxi province, north China. The type population of L. piceae sp. n. is characterised by having females 642-807 μm long, the cephalic region with six labial sectors divided by ribs, stylet 12-14 μm long, lateral field with four incisures, postvulval uterine sac (PUS) 114-161 μm long, vulva with a well-developed anterior flap, tail with a single stalk at tip, bearing four pedunculate tubercles, each tubercle including 5-7 finger-like protrusions; males spicules 18-24 μm long and three pairs of caudal papillae present. The new species looks closely similar to L. persicus, representing its cryptic species, being separated by differences in some morphological indices and partial large subunit (LSU) rDNA sequences. Its morphological differences from other relevant species were discussed. L. sinensis was also recorded from Shanxi province for the first time. The phylogenetic relationships of the recovered populations were reconstructed using sequences of the near full length small subunit (SSU) and D2-D3 segments of LSU rDNA, and the relationships of both species were discussed.

Molecular phylogeny and new insight into the stomatal complexity of Fictor platypapillata sp. n. (Diplogastridae: Nematoda) associated with Oniticellus cinctus (Coleoptera: Scarabaeidae)

The new species Fictor platypapillata was isolated from dung beetle Oniticellus cinctus (Scarabaeidae), collected from the district Balrampur, Uttar Pradesh, India. Fictor platypapillata sp. n. is described based on morphology, morphometric and molecular characterization, supplemented with scanning electron microscopy observations. The new species is characterized by two female morphs based on stomatal dimorphism: α morph with left subventral wall having 14 denticles, six low conical and eight elongated finger-like, slender denticles separated by a deep groove; inner wall of gymnostom with linearly arranged warts; β morph with inner wall of gymnostom lacking warts; dorsal and right subventral stegostomal walls having large, slender teeth with hook-shaped apical end. Genital sensilla eight pairs with v5 pair flattened, button-shaped, located ventrally. The phylogenetic analyses revealed significant congruence, especially in the position of the subordinate taxa of genus Fictor that shows polyphyly by both Bayesian inference and minimum evolution methods. The taxonomy of the genus is updated with a valid species list along with their geographical mapping.

TARANTOBELUS JEFFDANIELSI N. SP. (PANAGROLAIMOMORPHA; PANAGROLAIMIDAE), A NEMATODE PARASITE OF TARANTULAS

Multiple tarantula deaths for a wholesale breeder were reported in 2018. The breeder noticed white discharge in the oral cavities of the tarantulas. Upon inspection, it was discovered that the white discharge was a large group of nematodes intertwined inside the tarantula's oral cavity. We examined the nematodes and propose a new species, Tarantobelus jeffdanielsi n. sp., in the currently monotypic genus Tarantobelus based on a combination of morphological and morphometrical data and unique nuclear rDNA 28S and 18S sequences. Based on phylogenetic analyses, the previously described Tarantobelus arachnicida was relocated, along with T. jeffdanielsi, into the family Panagrolaimidae. We also provide evidence of the ability of T. jeffdanielsi to parasitize Galleria mellonella larvae and the tarantula Grammostola pulchra. The life span and fecundity of the new species were also assessed, resulting in an 11.2-d average life span, and a total fertility rate of 158 nematodes/adult.

New Zealand species of the genus Tripyla Bastian, 1865 (Nematoda:Triplonchida: Tripylidae). I : A new species, a new record and key to long-tailed species

This paper describes two species of the genus of Tripyla from New Zealand and also provides a key to species based on the morphology of females in eight long-tailed (c < 5) species in the genus of Tripyla. Tripyla bioblitz sp. nov. is characterized by its more anterior vulva position (V = 43.7–45.4%), relatively short body length (1150–1410 μm) and long tail (c = 4.0–4.4) in the group. Tripyla filicaudata de Man, 1880 is recorded for the first time from New Zealand and from the Southern Hemisphere. In addition, the phylogenetic relationships among species were analyzed using data from the near full length small subunit (SSU) and D2/D3 expansion segments of the large subunit ribosomal (LSU) rRNA genes, and these analyses revealed that T. bioblitz sp. nov. is close to but distinct from T. filicaudata de Man, 1880.

Steinernema diaprepesi Nguyen & Duncan (Rhabditida: Steinernematidae), a new entomopathogenic nematode from Brazil

Entomopathogenic nematodes (EPNs) can control pests due to their mutual association with bacteria. The use of these biological control agents is increasing worldwide due to advances in research about its control efficiency, range of action and mass production. The identification of EPNs adapted to specific environmental and climatic conditions is important for sustainable pest suppression in integrated management (IPM) programs. The objective is to report, for the first time, the occurrence of the Steinernema diaprepesi in Brazil. Steel mesh traps with Galleria mellonella Linnaeus (Lepidoptera: Pyralidae) larvae were buried in red latosol cultivated with Eucalyptus. Infective juveniles (IJs) were isolated from dead larvae and multiplied in healthy ones of this host to confirm its pathogenicity and to start a laboratory population from the strain found in the field. The DNA of the IJs was extracted and amplified using PCR technique with the universal primers D2A and D3B. The detection of S. diaprepesi is the first report of this nematode in Brazil, increasing the knowledge about its distribution in the world and the diversity of EPNs that must be considered as agents of biological pest control in the country.

Fast genetic mapping using insertion-deletion polymorphisms in Caenorhabditis elegans

Genetic mapping is used in forward genetics to narrow the list of candidate mutations and genes corresponding to the mutant phenotype of interest. Even with modern advances in biology such as efficient identification of candidate mutations by whole-genome sequencing, mapping remains critical in pinpointing the responsible mutation. Here we describe a simple, fast, and affordable mapping toolkit that is particularly suitable for mapping in Caenorhabditis elegans. This mapping method uses insertion-deletion polymorphisms or indels that could be easily detected instead of single nucleotide polymorphisms in commonly used Hawaiian CB4856 mapping strain. The materials and methods were optimized so that mapping could be performed using tiny amount of genetic material without growing many large populations of mutants for DNA purification. We performed mapping of previously known and unknown mutations to show strengths and weaknesses of this method and to present examples of completed mapping. For situations where Hawaiian CB4856 is unsuitable, we provide an annotated list of indels as a basis for fast and easy mapping using other wild isolates. Finally, we provide rationale for using this mapping method over other alternatives as a part of a comprehensive strategy also involving whole-genome sequencing and other methods.

Analysis of C. elegans acetylcholine synthesis mutants reveals a temperature-sensitive requirement for cholinergic neuromuscular function

In Caenorhabditis elegans, the cha-1 gene encodes choline acetyltransferase (ChAT), the enzyme that synthesizes the neurotransmitter acetylcholine. We have analyzed a large number of cha-1 hypomorphic mutants, most of which are missense alleles. Some homozygous cha-1 mutants have approximately normal ChAT immunoreactivity; many other alleles lead to consistent reductions in synaptic immunostaining, although the residual protein appears to be stable. Regardless of protein levels, neuromuscular function of almost all mutants is temperature sensitive, i.e., neuromuscular function is worse at 25° than at 14°. We show that the temperature effects are not related to acetylcholine release, but specifically to alterations in acetylcholine synthesis. This is not a temperature-dependent developmental phenotype, because animals raised at 20° to young adulthood and then shifted for 2 hours to either 14° or 25° had swimming and pharyngeal pumping rates similar to animals grown and assayed at either 14° or 25°, respectively. We also show that the temperature-sensitive phenotypes are not limited to missense alleles; rather, they are a property of most or all severe cha-1 hypomorphs. We suggest that our data are consistent with a model of ChAT protein physically, but not covalently, associated with synaptic vesicles; and there is a temperature-dependent equilibrium between vesicle-associated and cytoplasmic (i.e., soluble) ChAT. Presumably, in severe cha-1 hypomorphs, increasing the temperature would promote dissociation of some of the mutant ChAT protein from synaptic vesicles, thus removing the site of acetylcholine synthesis (ChAT) from the site of vesicular acetylcholine transport. This, in turn, would decrease the rate and extent of vesicle-filling, thus increasing the severity of the behavioral deficits.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1-D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631-641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

Morphological and molecular characterization of Epidorylaimus procerus sp. n. (Dorylaimida: Qudsianematidae) from Vietnam

Epidorylaimus procerus sp. n., collected from a natural habitat in Vietnam, is described and illustrated. It is distinguishable by its 2.16 to 2.46-mm-long body, lip region offset by depression and 15 to 17-µm broad, odontostyle 32 to 35-µm long, neck 415 to 461-µm long, pharyngeal expansion occupying 47 to 52% of the total neck length, uterus 76 to 130-µm long or 1.0 to 1.5-body diameters, vulva transverse (V = 40-43), caudal region conical elongate (157-186 µm, c =12.1-14.4, c′ = 4.4-5.5) with blister-like bodies, and hyaline portion occupying one-fourth its length, and males absent. Molecular analysis shows a close relationship of the new species and E. lugdunensis, supporting monophyly of the genus Epidorylaimus.

ERdj8 governs the size of autophagosomes during the formation process

In macroautophagy, membrane structures called autophagosomes engulf substrates and deliver them for lysosomal degradation. Autophagosomes enwrap a variety of targets with diverse sizes, from portions of cytosol to larger organelles. However, the mechanism by which autophagosome size is controlled remains elusive. We characterized a novel ER membrane protein, ERdj8, in mammalian cells. ERdj8 localizes to a meshwork-like ER subdomain along with phosphatidylinositol synthase (PIS) and autophagy-related (Atg) proteins. ERdj8 overexpression extended the size of the autophagosome through its DnaJ and TRX domains. ERdj8 ablation resulted in a defect in engulfing larger targets. C. elegans, in which the ERdj8 orthologue dnj-8 was knocked down, could perform autophagy on smaller mitochondria derived from the paternal lineage but not the somatic mitochondria. Thus, ERdj8 may play a critical role in autophagosome formation by providing the capacity to target substrates of diverse sizes for degradation.

Morphological, molecular and ecological characterization of a native isolate of Steinernema feltiae (Rhabditida: Steinernematidae) from southern Chile

Background

Steinernema feltiae is an entomopathogenic nematode used in biological control programs with a global distribution. Populations of this species show phenotypic plasticity derived from local adaptation and vary in different traits, such as location and host penetration. The aim of this work was to describe a Chilean isolate of this nematode species, using integrative approaches.

Methods

Nematode morphological and morphometric studies were conducted along with molecular analysis of nuclear genes. The symbiotic bacterium was also identified by sequencing the 16S rRNA gene. Some ecological characteristics were described, including the temperature requirements for the nematode life cycle and the effect of soil water content for optimal reproduction.

Results

Morphometric characterization revealed a large intra-specific variability. The isolate identity was also corroborated with the analysis of nuclear genes. Based on the 16S gene, its symbiont bacteria, Xenorhabdus bovienii, was identified. The lowest, optimal and highest temperatures found to limit the infestation and reproduction on Galleria mellonella were 10, 20 and 30 °C, respectively; the emergence from the host larvae occurred approximately 10 days after inoculation. Differences were observed in offspring, and 120 infective juveniles (IJ)/larva was the most prolific dose at 20 °C. The soil water content did not affect the number of IJ invaders, penetration efficacy and IJ emergence time or offspring per larva, but it caused a delay in achieving full mortality at the permanent wilting point with respect to saturation and field capacity.

Conclusions

For the first time, a Chilean isolate of S. feltiae is described in detail considering morphological, molecular and ecological aspects. The isolate was shown to be efficient in soil containing water, with optimal temperatures ranging from 15 to 25 °C for host infestation and production of an abundant offspring; these characteristics would allow its potential use as control agents in a wide geographical area of the country.

Insights on foodborne zoonotic trematodes in freshwater snails in North and Central Vietnam

Foodborne zoonotic trematode (FZT) infections are common neglected tropical diseases in Southeast Asia. Their complicated life cycles involve freshwater snails as intermediate hosts. A cross-sectional study was conducted in Yen Bai and Thanh Hoa provinces in North and Central Vietnam, to investigate the diversity of cercariae of potential FZT and to construct the phylogenetic relationship of trematode cercariae based on the Internal Transcribed Spacer 2 (ITS2) region. Among 17 snail species collected from various habitats, 13 were infected by 10 cercarial groups among which parapleurolophocercous, pleurolophocercous, and echinostome cercariae were of zoonotic importance. The monophyletic tree separated cercarial sequences into different groups following the description of the cercariae families in which Haplorchidae, Opisthorchiidae, Echinochasmidae, and Echinostomatidae are important families of FZT. The overall prevalence was different among snail species and habitats and showed a seasonal trend. Parapleurolophocercous and echinostome cercariae emerged as the most common cercariae in snails in Yen Bai, while monostome, echinostome, and megalura cercariae were most common in Thanh Hoa. Using a molecular approach, we identified Parafossarulus striatulus as the first intermediate snail host of Clonorchis sinensis in Thac Ba Lake. Melanoides tuberculata and Bithynia fuchsiana were we identified preferred intermediate snail hosts of a diverse range of trematode species including intestinal flukes (i.e., Haplorchis pumilio and Echinochasmus japonicus) in Yen Bai and Thanh Hoa, respectively.

Molecular and Morphological Diversity of Heterodesmus Brady and Its Phylogenetic Position within Cypridinidae (Ostracoda)

Ostracod genus Heterodesmus Brady, 1866 is known thus far to contain only three species: H. adamsii Brady, 1866; H. apriculus Hiruta, 1992; and H. naviformis (Poulsen, 1962). This genus has been recorded from the Sea of Japan, and the coastal areas of Thailand and Vietnam. The main generic character is the presence of antero-dorsal and postero-dorsal tube-like processes on the rostrum on both valves. The three species mostly differ in the shell lateral projections. Their relationship and the position of Heterodesmus within family Cypridinidae are poorly understood, partly due to the lack of publication of DNA data so far. We study Heterodesmus collected from several localities in the Northwest Pacific, namely Tsushima and Iki Islands in Japan and Maemul Island in Korea. Besides morphological characters, we also use two mitochondrial markers (16S rRNA and mtCOI) and three nuclear regions (18S rRNA, 28S rRNA, and internal transcribed spacer - ITS) in the samples to detect the biodiversity of this genus. Our phylogenetic tree based on molecular data coupled with morphology reveals the presence of two species, H. adamsii and H. apriculus. We report on their morphological variability, molecular diversity, and phylogenetic position within Cypridinidae based on 16S, 28S and 18S rRNAs, and provide a taxonomic key for all living genera of this family. For the first time, we give an overview of the intrageneric and intrafamily DNA distances of the above markers for the entire subclass Myodocopa.

Nematodes associated with terrestrial slugs in the Edmonton region of Alberta, Canada

A survey of nematodes associated with terrestrial slugs was conducted in residential gardens, nurseries, greenhouses and agricultural sites located in and around Edmonton, Alberta, Canada. A total of 2406 slugs were collected from 82 sites. Slugs were decapitated and cadavers were incubated for two weeks, with emerging nematodes removed and processed for identification. Nematodes were identified using molecular sequence data for the 18S ribosomal DNA. Nematodes were recovered from 20 of the 82 sites surveyed, with 24.4% of the slugs infected with nematodes. A total of seven nematodes were identified to species level, including Caenorhabditis elegans, Panagrolaimus papillosus, Pellioditis typica, Pelodera pseudoteres, Rhabditella axei, Rhabditoides inermiformis and Phasmarhabditis californica. An additional four specimens were identified to genus level, including Oscheius sp. (9), Pristionchus sp., Rhabditis sp. and Rhabditophanes sp. (1). The two most common nematode species were C. elegans and P. pseudoteres. The facultative parasite, P. californica, was recovered from a single Arion rufus specimen, collected from a seasonal nursery. To our knowledge, this study represents the first survey of slug-associated nematodes in Canada.

Conserved statin-mediated activation of the p38-MAPK pathway protects Caenorhabditis elegans from the cholesterol-independent effects of statins

OBJECTIVE

Statins are a group of medications that reduce cholesterol synthesis by inhibiting the activity of HMG-CoA reductase, a key enzyme in the mevalonate pathway. The clinical use of statins to lower excess cholesterol levels has revolutionized the cardiovascular field and increased the survival of millions, but some patients have adverse side effects. A growing body of data suggests that some of the beneficial and adverse effects of statins, including their anti-inflammatory, anti-tumorigenic, and myopathic activities, are cholesterol-independent. However, the underlying mechanisms for these effects of statins are not well defined.

METHODS

Because Caenorhabditis elegans (C. elegans) lacks the cholesterol synthesis branch of the mevalonate pathway, this organism is a powerful system to unveil the cholesterol-independent effects of statins. We used genetic and biochemical approaches in C. elegans and cultured macrophage-derived murine cells to study the cellular response to statins.

RESULTS

We found that statins activate a conserved p38-MAPK (p38) cascade and that the protein geranylgeranylation branch of the mevalonate pathway links the effect of statins to the activation of this p38 pathway. We propose that the blockade of geranylgeranylation impairs the function of specific small GTPases we identified as upstream regulators of the p38 pathway. Statin-mediated p38 activation in C. elegans results in the regulation of programs of innate immunity, stress, and metabolism. In agreement with this regulation, knockout of the p38 pathway results in the hypersensitivity of C. elegans to statins. Treating cultured mammalian cells with clinical doses of statins results in the activation of the same p38 pathway, which upregulates the COX-2 protein, a major regulator of innate immunity in mammals.

CONCLUSIONS

Statins activate an evolutionarily conserved p38 pathway to regulate metabolism and innate immunity. Our results highlight the cytoprotective role of p38 activation under statin treatment in vivo and propose that this activation underlies many of the critical cholesterol-independent effects of statins.

Phylogenetic evidence for the invasion of a commercialized European Phasmarhabditis hermaphrodita lineage into North America and New Zealand

Biological control (biocontrol) as a component of pest management strategies reduces reliance on synthetic chemicals, and seemingly offers a natural approach that minimizes environmental impact. However, introducing a new organism to new environments as a classical biocontrol agent can have broad and unanticipated biodiversity effects and conservation consequences. Nematodes are currently used in a variety of commercial biocontrol applications, including the use of Phasmarhabditis hermaphrodita as an agent targeting pest slug and snail species. This species was originally discovered in Germany, and is generally thought to have European origins. P. hermaphrodita is sold under the trade name Nemaslug®, and is available only in European markets. However, this nematode species was discovered in New Zealand and the western United States, though its specific origins remained unclear. In this study, we analyzed 45 nematode strains representing eight different Phasmarhabditis species, collected from nine countries around the world. A segment of nematode mitochondrial DNA (mtDNA) was sequenced and subjected to phylogenetic analyses. Our mtDNA phylogenies were overall consistent with previous analyses based on nuclear ribosomal RNA (rRNA) loci. The recently discovered P. hermaphrodita strains in New Zealand and the United States had mtDNA haplotypes nearly identical to that of Nemaslug®, and these were placed together in an intraspecific monophyletic clade with high support in maximum likelihood and Bayesian analyses. We also examined bacteria that co-cultured with the nematode strains isolated in Oregon, USA, by analyzing 16S rRNA sequences. Eight different bacterial genera were found to associate with these nematodes, though Moraxella osloensis, the bacteria species used in the Nemaslug® formulation, was not detected. This study provided evidence that nematodes deriving from the Nemaslug® biocontrol product have invaded countries where its use is prohibited by regulatory agencies and not commercially available.

Steinernema diaprepesi (Rhabditida: Steinernematidae) parasitizing Gonipterus platensis (Coleoptera: Curculionidae)

Entomopathogenic nematodes (EPNs) can control pests due to mutualistic association with bacteria that reproduce and kill the host from septicemia, making the environment favourable for nematode development and reproduction. The objective of this study was to identify an EPN isolate collected in eucalyptus cultivation and to determine its pathogenicity with regard to Gonipterus platensis Marelli (Coleoptera: Curculionidae). Four steel-mesh traps with two seventh-instar Galleria mellonella larvae were buried 5 cm deep in the soil in a commercial Eucalyptus plantation. After 7 days, the traps were packed in plastic bags and transported to laboratory to isolate the EPNs using White traps. The obtained nematodes were multiplied in G. mellonella larvae and identified by sequencing their D2/D3 expansion of the 28S rDNA region by polymerase chain reaction (PCR) and specific primers for ITS regions. Steinernema diaprepesi was identified and inoculated into G. platensis pupae at doses of 500, 1000 and 5000 infective juveniles (IJs) to determine its pathogenicity to this pest. At 8 days after inoculation, the mortality rate of the G. platensis pupae was 80% with the lowest concentration and 100% with the others. The emergence of nematodes and the rapid degradation of G. platensis pupae were observed in those inoculated with IJs. The pathogenicity to the G. platensis pupae indicates potential for using this nematode in the integrated management of this insect.

Genetic Diversity of the root-knot nematode Meloidogyne enterolobii in Mulberry Based on the Mitochondrial COI Gene

This study explores the genetic diversity and structure of Meloidogyne enterolobii in mulberry in China. The COI mitochondrial gene (mtCOI) in M.enterolobii populations in Guangdong, Guangxi, and Hunan Provinces was PCR-amplified, sequenced, and analyzed for genetic diversity. The total number of variations, haplotypes (Hap), the average number of nucleotide differences (k), haplotype diversity (H), and nucleotide diversity (π) of mtCOI were 25, 11, 4.248, 0.900, and 0.00596, respectively. Insignificant differences in Fst value (0.0169) and a high level of gene flow (7.02) were detected among the 19-mulberry root-knot nematode populations, and high genetic variation within each population and a small genetic distance among populations were observed. Both phylogenetic analyses and network mapping of the 11 haplotypes revealed a dispersed distribution pattern of 19 mulberry root-knot nematode populations and an absence of branches strictly corresponding to the 19 range sampling sites. The neutrality test and mismatch analysis indicated that mulberry root-knot nematode populations experienced a population expansion in the past. The analysis of molecular variance (AMOVA) revealed that the genetic differentiation of M. enterolobii was mainly contributed by the variation within each group. No significant correlation was found between the genetic distance and geographical distance of M. enterolobii populations. The findings of this study provide a profound understanding of the M. enterolobii population and will inform the development of strategies to combat and manage root-knot nematodes in mulberry.

Alien parasites on an alien fish species: monogeneans from the black bullhead Ameiurus melas (Siluriformes) in the Lake Srebarna Biosphere Reserve, Bulgaria, with the first record of Gyrodactylus nebulosus in the Palaearctic

Black bullhead Ameiurus melas (Actinopterygii: Siluriformes) is an alien fish species of North American origin, which has expanded its invasive geographical range in Europe. In 2017-2019, 32 black bullhead specimens from the Lake Srebarna Biosphere Reserve, Bulgaria, were examined for monogenean parasites. Two species of monogeneans were recorded and identified on the basis of morphological and molecular data: Ligictaluridus pricei (Ancyrocephalidae), with prevalence 100% and intensity 2-32 (mean 13.3 ± 6.8), and Gyrodactylus nebulosus (Gyrodactylidae), with prevalence 72.0% and intensity 1-15 (mean 7.4 ± 4.3). Partial 18S rDNA and the ITS1 region of L. pricei were sequenced. For G. nebulosus, sequenced genes included the partial 18S rDNA and the entire ITS1-5.8S rDNA-ITS2 region as well as the mitochondrial COI gene. Both recorded monogenean species are specific parasites of North American ictalurid fishes and alien to Europe. The present study is the first record of L. pricei from Bulgaria and the first record of G. nebulosus from Europe and the Palaearctic Region.

Two species of Thoracostomopsidae (Nematoda: Enoplida) from Jeju Island, South Korea

During a survey of intertidal zones at beaches on Jeju Island, two species belonging to the family Thoracostomopsidae were discovered. One new species, Enoploides koreanus sp. nov. and one known species, Epacanthion hirsutumShi & Xu, 2016 are reported. Along with morphological analysis, mitochondrial cytochrome oxidase c subunit 1 (mtCOI) sequences and 18S rRNA sequences of the species were also obtained and used to check relative p-distance and phylogenetic positions. While most species of Enoploides have long spicules, the new species belongs to a group of Enoploides with short spicules < 150 µm). Of the seven species with short spicules, the new species is most closely related to E. disparilisSergeeva, 1974. They both have similar body length, fairly similar sized and shaped spicules with small gubernaculum running parallel to distal end of spicule, and an index value of b. The new species can be distinguished from E. disparilis by having pre-anal supplementary organ with short conical tail, while E. disparilis lacks pre-anal supplementary organ and has a long conico-cylindrical tail. Along with the description of the new species, the genus EnoploidesSsaweljev, 1912 is bibliographically reviewed and revised. Of 45 species described to date, 27 are now considered valid, 16 species inquirendae due to inadequate descriptions and ambiguity of the material examined, along with two cases of nomen nudum. With this review, we provide an updated diagnosis and list of valid species, a tabular key comparing diagnostic characters of all valid species, and a new complete key to species. One known species, Epacanthion hirsutumShi & Xu, 2016, is reported in Korea for the first time. The morphology agrees well with the original description provided by Shi & Xu, 2016. As they had already reviewed the genus at the time of reporting four Epacanthion species, we provide only a description, depiction, and measurements for comparison purposes.

A new species of the genusSarsamphiascusHuys, 2009 (Copepoda: Harpacticoida: Miraciidae) from a sublittoral zone of Hawaii

A new species of SarsamphiascusHuys, 2009 was collected from sandy sediments of Hawaii at 12 –18 m depth. While the new species, Sarsamphiascus hawaiiensis sp. nov., is morphologically most closely related to S. kawamurai (Ueda & Nagai, 2005), the two species can be distinguished by the combination of the following morphological characteristics: elongated segments of the antennule in the new species, type of outer setae of the P5 exopod (bare in S. kawamurai), position of the inner seta of the P5 exopod in both sexes (more proximal in S. kawamurai), length and type of the setae of female P6 (shorter and bare in S. kawamurai). This is the first species of Sarsamphiascus from Hawaii to be discovered. Molecular analyses of mitochondrial cytochrome c oxidase subunit I (mtCOI) and nuclear 18S ribosomal RNA (18S rRNA) genes confirmed that S. hawaiiensis and S. kawamurai are distinct species.

Characterization of root-knot nematodes infecting mulberry in Southern China

China is one of the largest producers of mulberry in the world. With the development of the sericulture industry, several pests and diseases have occurred in rapid succession, chief among which is the root-knot nematode disease affecting mulberry. According to the China cocoon and silk exchange, cocoon prices have doubled since the beginning of 2009 and rose to 92,700 yuan ($135,770) per tonne in mid-April 2010. According to customs statistics, in the first eight months of 2011, China's silk merchandise exports amounted to 2.39 billion yuan. In this study, sequencing of the rDNA-ITS and D2-D3 region of the 28S rRNA gene was combined with root-knot nematode morphological characteristics to identify the root-knot nematode infecting mulberry in the Guangdong, Guangxi, and Hunan provinces of China. This resulted in the identification of Meloidogyne enterolobii as the causal species of root-knot nematode infections in these regions. Importantly, the morphological data agreed completely with our molecular phenotyping efforts, indicating that rDNA sequencing could provide a more clear-cut and less labor-intensive means of characterizing root-knot nematode infections in the future. The differences between this study and the previous studies were discussed, as well as the damage degree, host species and influence scope of M. enterolobii.

China is one of the largest producers of mulberry in the world. With the development of the sericulture industry, several pests and diseases have occurred in rapid succession, chief among which is the root-knot nematode disease affecting mulberry. According to the China cocoon and silk exchange, cocoon prices have doubled since the beginning of 2009 and rose to 92,700 yuan ($135,770) per tonne in mid-April 2010. According to customs statistics, in the first eight months of 2011, China’s silk merchandise exports amounted to 2.39 billion yuan. In this study, sequencing of the rDNA-ITS and D2-D3 region of the 28S rRNA gene was combined with root-knot nematode morphological characteristics to identify the root-knot nematode infecting mulberry in the Guangdong, Guangxi, and Hunan provinces of China. This resulted in the identification of Meloidogyne enterolobii as the causal species of root-knot nematode infections in these regions. Importantly, the morphological data agreed completely with our molecular phenotyping efforts, indicating that rDNA sequencing could provide a more clear-cut and less labor-intensive means of characterizing root-knot nematode infections in the future. The differences between this study and the previous studies were discussed, as well as the damage degree, host species and influence scope of M. enterolobii.

Genetic interactions between the DBL-1/BMP-like pathway and dpy body size-associated genes in Caenorhabditis elegans

Bone morphogenetic protein (BMP) signaling pathways control many developmental and homeostatic processes, including cell size and extracellular matrix remodeling. An understanding of how this pathway itself is controlled remains incomplete. To identify novel regulators of BMP signaling, we performed a forward genetic screen in Caenorhabditis elegans for genes involved in body size regulation, a trait under the control of BMP member DBL-1. We isolated mutations that suppress the long phenotype of lon-2, a gene that encodes a negative regulator that sequesters DBL-1. This screen was effective because we isolated alleles of several core components of the DBL-1 pathway, demonstrating the efficacy of the screen. We found additional alleles of previously identified but uncloned body size genes. Our screen also identified widespread involvement of extracellular matrix proteins in DBL-1 regulation of body size. We characterized interactions between the DBL-1 pathway and extracellular matrix and other genes that affect body morphology. We discovered that loss of some of these genes affects the DBL-1 pathway, and we provide evidence that DBL-1 signaling affects many molecular and cellular processes associated with body size. We propose a model in which multiple body size factors are controlled by signaling through the DBL-1 pathway and by DBL-1-independent processes.

CRISPR-Cas9-Guided Genome Engineering in Caenorhabditis elegans

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein) system is being used successfully for efficient and targeted genome editing in various organisms, including the nematode Caenorhabditis elegans. Recent studies have developed a variety of CRISPR-Cas9 approaches to enhance genome engineering via two major DNA double-strand break repair pathways: nonhomologous end joining and homologous recombination. Here, we describe a protocol for Cas9-mediated C. elegans genome editing together with single guide RNA (sgRNA) and repair template cloning (canonical marker-free and cassette selection methods), as well as injection methods required for delivering Cas9, sgRNAs, and repair template DNA into the germline. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Guide RNA preparation Alternate Protocol 1: sgRNA cloning using fusion PCR Basic Protocol 2: Preparation of a repair template for homologous recombination Alternate Protocol 2: Preparation of repair template donors for the cassette selection method Basic Protocol 3: Injecting animals Basic Protocol 4: Screening transgenic worms with marker-free method Alternate Protocol 3: Screening transgenic worms with cassette selection method.

Visualization and Quantification of Transposon Activity in Caenorhabditis elegans RNAi Pathway Mutants

RNA silencing pathways play critical roles in maintaining quiescence of transposons in germ cells to promote genome integrity. However the precise mechanism by which different types of transposons are recognized by these pathways is not fully understood. Furthermore, the location in the germline where this transposition occurs after disruption of transposon silencing was previously unknown. Here we utilize the spatial and temporal organization of the Caenorhabditis elegans germline to demonstrate that transposition of DNA transposons in RNA silencing pathway mutants occur in all stages of adult germ cells. We further demonstrate that the double-strand breaks generated by transposons can restore homologous recombination in a mutant defective for the generation of meiosis-specific double-strand breaks. Finally, we detected clear differences in transposase expression and transposon excision between distinct branches of the RNA silencing pathway, emphasizing that there are multiple mechanisms by which transposons can be recognized and routed for small-RNA-mediated silencing.

New evidence of nematode-endosymbiont bacteria coevolution based on one new and one known dagger nematode species of Xiphinema americanum-group (Nematoda, Longidoridae)

Three populations of Xiphinema primum n. sp. and two populations of X. pachtaicum were recovered from natural forests and cultural regions of northern Iran. Both species belong to the X. americanum-group and were characterized by their morphological, morphometric and molecular data. The new species, which was recovered in three locations, belongs to the X. brevicolle-complex and is characterized by 2124–2981 μm long females with a widely rounded lip region separated from the rest of the body by a depression, 103–125 μm long odontostyle, two equally developed genital branches with endosymbiont bacteria inside the ovary, which are visible under light microscope (LM), vulva located at 51.8–58.0%, the tail is 26–37 μm long with a bluntly rounded end and four juvenile developmental stages. It was morphologically compared with nine similar species viz. X. brevicolle, X. diffusum, X. incognitum, X. himalayense, X. luci, X. parabrevicolle, X. paramonovi, X. parataylori and X. taylori. The second species, X. pachtaicum, was recovered in two geographically distant points close to city of Amol. Molecular phylogenetic studies of the new species were performed using partial sequences of the D2-D3 expansion segments of the large subunit ribosomal RNA gene (LSU rDNA D2-D3), the internal-transcribed spacer rDNA (ITS = ITS1+5.8S+ITS2), and the mitochondrial cytochrome c oxidase I gene (COI mtDNA) regions. The Iranian population of X. pachtaicum was also phylogenetically studied based upon its LSU rDNA D2-D3 sequences. Both species were also inspected for their putative endosymbiont bacteria. Candidatus Xiphinematobacter sp. was detected from two examined populations of the new species, whereas the second endosymbiont bacterium, detected from three examined isolates of X. pachtaicum, was related to the plant and fungal endosymbionts of the family Burkholderiaceae. The phylogenetic analyses of the two endosymbiont bacteria were performed using partial sequences of 16S rDNA. In cophylogenetic analyses, significant levels of cophylogenetic signal were observed using both LSU rDNA D2-D3 and COI mtDNA markers of the host nematodes and 16S rDNA marker of the endosymbiont bacteria.

Modern technologies and algorithms for scaffolding assembled genomes

The computational reconstruction of genome sequences from shotgun sequencing data has been greatly simplified by the advent of sequencing technologies that generate long reads. In the case of relatively small genomes (e.g., bacterial or viral), complete genome sequences can frequently be reconstructed computationally without the need for further experiments. However, large and complex genomes, such as those of most animals and plants, continue to pose significant challenges. In such genomes, assembly software produces incomplete and fragmented reconstructions that require additional experimentally derived information and manual intervention in order to reconstruct individual chromosome arms. Recent technologies originally designed to capture chromatin structure have been shown to effectively complement sequencing data, leading to much more contiguous reconstructions of genomes than previously possible. Here, we survey these technologies and the algorithms used to assemble and analyze large eukaryotic genomes, placed within the historical context of genome scaffolding technologies that have been in existence since the dawn of the genomic era.

MANF deletion abrogates early larval Caenorhabditis elegans stress response to tunicamycin and Pseudomonas aeruginosa

Mesencephalic astrocyte-derived neurotrophic factor (MANF) is the only human neurotrophic factor with an evolutionarily-conserved C. elegans homolog, Y54G2A.23 or manf-1. MANF is a small, soluble, endoplasmic-reticulum (ER)-resident protein that is secreted upon ER stress and promotes survival of target cells such as neurons. However, the role of MANF in ER stress and its mechanism of cellular protection are not clear and the function of MANF in C. elegans is only beginning to emerge. In this study, we show that depletion of C. elegans manf-1 causes a slight decrease in lifespan and brood size; furthermore, combined depletion of manf-1 and the IRE-1/XBP-1 ER stress/UPR pathway resulted in sterile animals that did not produce viable progeny. We demonstrate upregulation of markers of ER stress in L1 larval nematodes, as measured by hsp-3 and hsp-4 transcription, upon depletion of manf-1 by RNAi or mutation; however, there was no difference in tunicamycin-induced expression of hsp-3 and hsp-4 between wild-type and MANF-deficient worms. Surprisingly, larval growth arrest observed in wild-type nematodes reared on tunicamycin is completely prevented in the manf-1 (tm3603) mutant. Transcriptional microarray analysis revealed that manf-1 mutant L1 larvae exhibit a novel modulation of innate immunity genes in response to tunicamycin. The hypothesis that manf-1 negatively regulates the innate immunity pathway is supported by our finding that the development of manf-1 mutant larvae compared to wild-type larvae is not inhibited by growth on P. aeruginosa. Together, our data represent the first characterization of C. elegans MANF as a key modulator of organismal ER stress and immunity.

Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems

Nematodes belong to one of the most diverse animal phyla. However, functional genomic studies in nematodes, other than in a few species, have often been limited in their reliability and success. Here we report that by combining liposome-based technology with microinjection, we were able to establish a wide range of genomic techniques in the newly described nematode genus Auanema. The method also allowed heritable changes in dauer larvae of Auanema, despite the immaturity of the gonad at the time of the microinjection. As proof of concept for potential functional studies in other nematode species, we also induced RNAi in the free-living nematode Pristionchus pacificus and targeted the human parasite Strongyloides stercoralis.

PCR amplification of a long rDNA segment with one primer pair in agriculturally important nematodes

Ribosomal DNA has been a reliable source of taxonomic and phylogenetic markers due to its high copy number in the genome and stable variation with few polymorphisms due to the homogenizing effect of concerted evolution. Typically specific regions are amplified through polymerase chain reaction (PCR) with multiple primer pairs that generate often incomplete and overlapping regions between adjacent segments of 18S, ITS1, 5.8S, ITS2, and 28S rDNA nucleotide sequences when combined in tandem. To improve the efficiency of this effort, a strategy for generating all these molecular sequences at once through PCR amplification of a large ribosomal 3.3 to 4.2 kb DNA target was developed using primer 18S-CL-F3 paired with D3B or a new alternative 28S PCR primer (28S-CL-R) and other well-positioned and ribosomal-specific sequencing primers (including novel primers 18S-CL-F7, 18S-CL-R6, 18S-CL-R7, 18S-CL-F8, 5.8S-CL-F1, 5.8S-CL-R1, 28S-CL-F1, 28S-CL-R3, 28S-CL-F3, 28S-CL-R1, and 28S-CL-F2). The D1 region between ITS2 and 28S boundaries and the flanking sequence between 18S and ITS1 boundaries were fully revealed in this large nucleotide segment. To demonstrate the value of this strategy, the long rDNA segment was amplified and directly sequenced in 17 agriculturally important nematodes from the Tylenchida, Aphelenchida, and Dorylaimida. The primers and their positions may be employed with traditional Sanger sequencing and with next-generation sequencing reagents and protocols.

Technical and economic efficiency of methods for extracting genomic DNA from Meloidogyne javanica

Plant parasitic nematodes reduce the production of agricultural crops. Species diagnosis is essential to predict losses, determine economic damage levels and develop integrated pest management programs. DNA extraction techniques need to be improved for precise and rapid molecular diagnosis of nematodes. The objective of the present study was to evaluate the efficiency of DNA extraction and amplification by PCR, cost and execution time by Chelex, Worm Lysis Buffer Method (WLB), Holterman Lysis Buffer Method (HLB) and FastDNA methods for nematodes of the Meloidogyne genus. The qualitative and quantitative efficiency of DNA extraction varied between methods. The band size of the amplified PCR product with WLB, Chelex and HLB methods was 590 bp. Extraction with the FastDNA is not recommended for DNA extraction from nematodes because it results in a low DNA concentration without bands in PCR amplification, besides presenting high cost. The efficiency of the WLB method to extracting DNA from Meloidogyne javanica was greater, ensuring a higher concentration and purity of the extracted material and guaranteeing lower costs and greater ease of PCR amplification.

Phylogenetic position of the parasitic nematode Trophomera (Nematoda, Benthimermithidae): A molecular analysis

Benthimermithid nematodes are parasites of invertebrates currently classified within their own order. Relationships between the Benthimermithida and other nematode orders, however, remain unclear due to their relatively simple morphology, their rarity, and paucity of molecular sequence data. Here, we combine molecular sequences obtained from Trophomera cf. marionensis in the Kermadec Trench with existing Trophomera sequences to determine the phylogenetic position of benthimermithids. Our SSU analyses showed Trophomera to be most closely-related to the order Plectida, subclass Chromadorea. Trophomera sequences formed a well-supported monophyletic clade placed within the Plectida, however relationships with other taxa within the order could not be resolved. Based on the result of these analyses, we propose that the family Benthimermithidae be moved to the order Plectida, however, future research on the classification of the family should focus on the benthimermithid genera Bathynema and Adenodelphis, for which no molecular sequences are yet available. We could not confirm a relationship between Trophomera and the family Camacolaimidae, which are both characterised by the presence of a stylet or stylet-like structure in the buccal cavity. Stylets are a common feature of parasitic nematodes, and its presence in a free-living benthimermithid ancestor perhaps similar to present-day camacolaimids could have facilitated a transition to a parasitic lifestyle. Our SSU phylogenetic analyses show that some features of benthimermithids, including the trophosome and a parasitic life cycle where the adults mate outside the host, have evolved independently in different groups of parasitic nematodes.

Comparative Genomics of Wolbachia-Cardinium Dual Endosymbiosis in a Plant-Parasitic Nematode

Wolbachia and Cardinium are among the most important and widespread of all endosymbionts, occurring in nematodes and more than half of insect and arachnid species, sometimes as coinfections. These symbionts are of significant interest as potential biocontrol agents due to their abilities to cause major effects on host biology and reproduction through cytoplasmic incompatibility, sex ratio distortion, or obligate mutualism. The ecological and metabolic effects of coinfections are not well understood. This study examined a Wolbachia-Cardinium coinfection in the plant-parasitic nematode (PPN), Pratylenchus penetrans, producing the first detailed study of such a coinfection using fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and comparative genomic analysis. Results from FISH and single-nematode PCR showed 123/127 individuals in a focal population carried Cardinium (denoted strain cPpe), and 48% were coinfected with Wolbachia strain wPpe. Both endosymbionts showed dispersed tissue distribution with highest densities in the anterior intestinal walls and gonads. Phylogenomic analyses confirmed an early place of cPpe and long distance from a sister strain in another PPN, Heterodera glycines, supporting a long history of both Cardinium and Wolbachia in PPNs. The genome of cPpe was 1.36 Mbp with 35.8% GC content, 1,131 predicted genes, 41% having no known function, and missing biotin and lipoate synthetic capacity and a plasmid present in other strains, despite having a slightly larger genome compared to other sequenced Cardinium. The larger genome revealed expansions of gene families likely involved in host-cellular interactions. More than 2% of the genes of cPpe and wPpe were identified as candidate horizontally transferred genes, with some of these from eukaryotes, including nematodes. A model of the possible Wolbachia-Cardinium interaction is proposed with possible complementation in function for pathways such as methionine and fatty acid biosynthesis and biotin transport.

Morphological and molecular characteristics of Parasitodiplogaster religiosae n. sp. (Nematoda: Diplogastrina) associated with Ficus religiosa in China

A new nematode species of the genus Parasitodiplogaster was recovered from syconia of Ficus religiosa at the Guangxiao Temple, Guangzhou, China. It is described herein as P. religiosae n. sp. and is characterised by possessing the longest and thinnest spicule of all currently described males in the genus, an elongated laterally “ε-shaped” and ventrally rhomboid-like gubernaculum, a stoma without teeth, consisting of a ring-like cheilostom with indistinct anteriolateral projections, a tube-like gymnostom and a funnel-like stegostom, monodelphic with a mean vulval position of 66%. There are three pre-cloacal and six post-cloacal male genital papillae with the arrangement P1, P2, P3, (C, P4), P5, P6d, P7, P8, P9d, Ph. This new species was easily differentiated from other members of the genus by DNA sequences of partial small subunit rRNA gene (SSU) and the D2-D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis also corroborated its reasonable placement within a well-supported monophyletic clade with other Parasitodiplogaster species and within the australis-group that includes P. australis and P. salicifoliae that are all associates of fig wasp pollinators (Platyscapa sp.) of figs of the subsection Urostigma.