The tapeworms of fishes (Chondrichthyes and Actinopterygii) account one-third (1670 from around 5000) of the total tapeworm (Platyhelminthes: Cestoda) species diversity. In total 1186 species from 9 orders occur as adults in elasmobranchs (sharks, rays and chimaeras), and 484 species from 8 orders mature in ray-finned fishes (referred to here as teleosts). Teleost tapeworms are dominated by freshwater species (78%), but only 3% of elasmobranch tapeworms are known from freshwater rays of South America and Asia (Borneo). In the last 2 decades, vast progress has been made in understanding species diversity, host associations and interrelationships among fish tapeworms. In total, 172 new species have been described since 2017 (149 from elasmobranchs and 23 from teleosts; invalidly described taxa are not included, especially those from the Oriental region). Molecular data, however, largely limited to a few molecular markers (mainly 28S rDNA, but also 18S and cox1), are available for about 40% of fish tapeworm species. They allowed us to significantly improve our understanding of their interrelationships, including proposals of a new, more natural classification at the higher-taxonomy level (orders and families) as well as at the lower-taxonomy level (genera). In this review, we summarize the main advances and provide perspectives for future research.

At a routine health check of a female peregrine falcon, 23 trematodes preliminary identified as Prosthogonimus sp. were removed from the bursa of Fabricius. Based on morphological and molecular examination, a new species, Prosthogonimus falconis, was described. The pear-shaped flukes were 4.3–6.9 mm long, with greatest width posterior to testes. Tegumental spines measuring between 17 and 21 μm long covered the whole body. Length and width ratio of oral to ventral suckers were 1:1.3. Extracaecal, multifollicular vitelline glands commenced prior to acetabulum and terminated posterior to testes. Eggs in the distal uterus measured 21 × 12 μm. Molecular analysis of internal transcribed spacer 2, cytochrome c oxidase subunit 1 and NADH dehydrogenase subunit 1 gene regions revealed that the new species described here is phylogenetically closest to Prosthogonimus cuneatus and Prosthogonimus pellucidus clusters.

Fascioliasis is a zoonotic disease caused by liver flukes transmitted by freshwater lymnaeid snails. Donkey and horse reservoir roles have been highlighted in human endemic areas. Liver fluke infection in mules has received very limited research. Their role in disease transmission, epidemiological importance and Fasciola hepatica pathogenicity are studied for the first time. Prevalence was 39.5% in 81 mules from Aconcagua, and 24.4% in 127 from Uspallata, in high-altitude areas of Mendoza province, Argentina. A mean amount of 101,242 eggs/mule/day is estimated. Lymnaeids from Uspallata proved to belong to ribosomal DNA internal transcribed spacer (ITS) markers ITS-1 and ITS-2 combined haplotype 3C of Galba truncatula. These lymnaeids were experimentally susceptible to infection by egg miracidia from mules. Infectivity, number of cercariae/snail and shedding period fit the enhanced F. hepatica/G. truncatula transmission pattern at very high altitude. This indicates that the mule is able to maintain the F. hepatica cycle independently. Individual burdens of 20 and 97 flukes were found. Mule infection susceptibility is intermediate between donkey and horse, although closer to the latter. Anatomo-pathology and histopathology indicate that massive infection may cause mule death. Haematological value decreases of red blood cells, haemoglobin, leucocytes and lymphocytes indicate anaemia and strong immunosuppression. Strongly increased biochemical marker values indicate liver function alterations. The mule probably played a role in the past exchanges with Chile and Bolivia through Mendoza province. Evidence suggests that mules could contribute to the spread of both F. hepatica and G. truncatula to human fascioliasis-endemic areas in these countries.

There is increasing evidence linking the gut microbiota to various aspects of human health. Nuts are a food rich in prebiotic fibre and polyphenols, food components which have been shown to have beneficial effects on the gut microbiota. This systematic review aimed to synthesise the evidence regarding the effect of nut consumption on the human gut microbiota. A systematic search of the databases MEDLINE, PubMed, Cochrane CENTRAL and CINAHL was performed until 28 November 2019. Eligible studies were those that investigated the effects of nut consumption in humans (aged over 3 years old), utilising next-generation sequencing technology. Primary outcome measures were between-group differences in α- and β-diversity metrics and gut microbial composition. A total of eight studies were included in the review. Included studies assessed the effects of either almonds, walnuts, hazelnuts or pistachios on the gut microbiota. Overall, nut consumption had a modest impact on gut microbiota diversity, with two studies reporting a significant shift in α-diversity and four reporting a significant shift in β-diversity. Walnuts, in particular, appeared to more frequently explain shifts in β-diversity, which may be a result of their unique nutritional composition. Some shifts in bacterial composition (including an increase in genera capable of producing SCFA: Clostridium, Roseburia, Lachnospira and Dialister) were reported following the consumption of nuts. Nut intake may yield a modulatory effect on the gut microbiota; however, results were inconsistent across studies, which may be explained by variations in trial design, methodological limitations and inter-individual microbiota.

Starch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

Echinococcus granulosus is the causative agent of cystic echinococcosis, which has serious impacts on human and/or animal health, resulting in significant economic losses. Echinococcus granulosus comprises a number of intra-specific variants or strains at the genetic level. In Saudi Arabia, few studies were performed on genetic variations in Echinococcus species. Therefore, the present study aimed to investigate the phenotypic and genetic characterization of hydatid cysts harboured by sheep and camels in Al-Madinah Al-Munawarah. Samples of hydatid cysts were collected from local sheep (n = 25) and camels (n = 8). The morphological criteria of protoscoleces were investigated. To investigate the molecular characterization, random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR), single-stranded conformation polymorphism (SSCP) were carried out. DNA was extracted from individual fertile cysts and subjected to RAPD-PCR analysis (using five arbitrary primers) and PCR amplification of cytochrome c oxidase I (cox1) and 12S ribosomal ribonucleic acid (12S rRNA) genes. The PCR products were subjected to SSCP analysis for genetic discrimination in E. granulosus isolates. In addition, partially sequencing of the mitochondrial DNA cox1 genes was achieved for assessing the phylogenetic positions of collected isolates using some global published sequence data of cox1 genes. The rostellar hooks of camel and local sheep isolates show remarkable variability in their dimensions. Five distinct SSCP patterns were identified in the 12S rRNA gene, showing intraspecific variations in E. granulosus of camels and local sheep. Sequencing of (cox1) genes of both local sheep and camels exhibit high similarity with those of the same gene (E. granulosus sensu stricto) published in NCBI BLAST.

Resistance to herbicides occurs in weeds as the result of evolutionary adaptation (Jasieniuk et al. 1996). Basically, two types of mechanisms are involved in resistance (Beckie and Tardif 2012; Délye 2013). Target-site resistance (TSR) is caused by changes in the tridimensional structure of the herbicide target protein that decrease herbicide binding, or by increased activity (e.g., due to increased expression or increased intrinsic activity) of the target protein. Nontarget-site resistance (NTSR) is endowed by any mechanism not belonging to TSR, e.g., reduction in herbicide uptake or translocation in the plant, or enhanced herbicide detoxification (reviewed in Délye 2013; Yuan et al. 2007).

The genetic basis of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weed research are currently meager compared with those available for many crops. Because genomic methodologies are becoming increasingly accessible and less expensive, the time is ripe for weed scientists to incorporate these methods into their research programs. One example is next-generation sequencing technology, which has the advantage of enhancing the sequencing output from the transcriptome of a weedy plant at a reduced cost. Successful implementation of these approaches will require collaborative efforts that focus resources on common goals and bring together expertise in weed science, molecular biology, plant physiology, and bioinformatics. We outline how these large-scale genomic programs can aid both our understanding of the biology of weedy and invasive plants and our success at managing these species in agriculture. The judicious selection of species for developing weed genomics programs is needed, and we offer up choices, but no Arabidopsis-like model species exists in the world of weeds. We outline the roadmap for creating a powerful synergy of weed science and genomics, given well-placed effort and resources.

The study reported in this Regional Research Communication aimed to analyse the genetic polymorphisms of β-casein in Chinese Holstein cows. β-casein has received considerable research interest in the dairy industry and animal breeding in recent years as a source not only of high quality protein, but also of bioactive peptides that may be linked to health effects. Morever, the polymorphic nature of β-casein and its association with milk production traits, composition, and quality also attracted several efforts in evaluating the allelic distribution of β-casein locus as a potential dairy trait marker. However, few data on beta-casein variants are available for the Chinese Holstein cow. In the present paper, one hundred and thirty three Holstein cows were included in the analysis. Results revealed the presence of 5 variants (A1, A2, A3, B and I), preponderance of the genotype A1A2 (0·353) and superiorities of A1/A2 alleles (0·432 and 0·459, respectively) in the population. Sequence analysis of β-casein gene in the cows showed four nucleotide changes in exon 7. Our study can provide reference and guidance for selection for superior milk for industrial applications and crossbreeding and genetic improvement programmes.

Mealybugs are major pests of grapevines worldwide. They cause economic losses by lowering the cosmetic value of fruits, reducing yields, transmitting viruses and resulting in the quarantine or rejection of produce in international trade. Knowledge of the species present in a vineyard is important for the adjustment of management strategies. We surveyed and accurately characterized the mealybugs infesting vineyards in one of the main production areas of Chile; 164 mealybugs were sampled from 26 vineyards in four regions of Chile and identified by DNA sequencing for two markers (cytochrome oxidase I and internal transcribed spacer 2) and morphological examination. Pseudococcus viburni (Signoret) was the most common species, followed by Pseudococcus meridionalis Prado and Pseudococcus cribata González. Molecular variability at the COI and ITS2 loci was observed in both P. viburni and P. cribata. A comparison of haplotypes of P. viburni worldwide provides support for a recent hypothesis that this species is native to South America, a finding with direct consequences for management. Neither Pseudococcus longispinus (Targioni & Tozzetti) nor Planococcus ficus Signoret were found.

Tersilochus obscurator Aubert and Tersilochus microgaster (Szépligeti) are larval endoparasitoids of economically-important stem-mining pests of winter oilseed rape (Brassica napus L.) in Europe. They are difficult to separate morphologically. Their hosts are Ceutorhynchus pallidactylus (Marsham) and Psylliodes chrysocephala Linnaeus, respectively. The parasitoids' taxonomic status, identification, host range and phenology were studied using genetic, morphometric and ecological data. The study used 527 female parasitoids from the UK and Germany, either field-collected in emergence traps or reared from field-collected host larvae. Two morphometric characters, the ovipositor sheath to first metasomal tergite ratio and the percentage of the mesopleuron spanned by the sternaulus, were measured. A 440 bp section of mitochondrial DNA cytochrome oxidase subunit I (COI) gene was sequenced from 35 parasitoids reared from C. pallidactylus, 20 reared from P. chrysocephala and individuals from two outgroups, Tersilochus heterocerus Thomson and Phradis interstitialis Thomson. Distinct and invariable COI sequences corresponded exclusively to each parasitoid group, confirming that T. obscurator and T. microgaster are discrete species. Measurements of host-reared and COI-sequenced specimens indicated that the ranges of both morphometric characters overlapped between species. Using these ranges as criteria, all but 3.6% of UK specimens and 2% of German specimens were identifiable to species without reference to host or phenology. There were differences in emergence phenology in the UK, adult T. microgaster emerging from winter diapause by 29 March 2000, T. obscurator emerging between 12 April and 24 May 2000. The value of molecular techniques in the identification of closely-related parasitoid species is discussed.

Dendrobium Sw., a member of the family Orchidaceae, includes approximately 1100 species distributed in different parts of the world. In China, the genus is represented by 76 species and two varieties, of which D. loddigesii, D. fimbriatum, D. chrysanthum, D. officinale (=D. candidum) and D. nobile are listed in the Chinese Pharmacopoeia as the source material for Herba Dendrobii (Shihu). Because of increased demand and high price, Herba Dendrobii is often adulterated in the trade by other related species. Many Dendrobium species are over-collected from the wild and are listed under endangered taxa in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Therefore, a reliable authentication method is needed to regulate the trade and help conserve the species from unscrupulous collections. This review describes the present status of using medicinal Dendrobium in China, current approaches to authenticate medicinal Dendrobium plants and Herba Dendrobii, and the efforts under way towards the development of DNA microarrays to facilitate differentiation/identification of genuine material in complex Chinese medicinal formulations.

Hammondia heydorni is regarded as a protozoan parasite that uses canids, e.g. dogs and foxes, as definitive hosts, but clinical signs of infection are rare. This study therefore took advantage of the opportunity to study an oocyst population from the faeces of a dog suffering from intermittent bouts of diarrhoea. Oocysts from the naturally infected dog were shown to be H. heydorni by using the polymerase chain reaction combined with DNA sequencing as a diagnostic tool.The nucleotide sequence data reported in this paper are available from GenBank under the following Accession numbers DQ183058, DQ183059 and DQ022687. A comparison of the first internal transcribed spacer (ITS1) sequence of ribosomal DNA obtained with those from other dog and fox oocysts, previously regarded as H. heydorni, showed these oocysts contained identical ITS1 sequences. However, the oocyst DNA from the fox and dog differed by the presence/absence of a 9 bp insertion/deletion within intron 1 of the alpha tubulin gene, and this difference was conserved across a number of different oocyst populations from the 2 species of host. A PCR assay was established that takes advantage of this insertion/deletion and is able to differentiate between the 2 oocyst populations. This study therefore provides evidence that H. heydorni oocysts from dogs and foxes represent 2 distinct genetic lineages that can be differentiated using a PCR, which targets the alpha tubulin locus.

Given a finite collection of strings of letters from a fixed alphabet, it is of interest, in the contexts of data compression and DNA sequencing, to find the length of the shortest string which contains each of the given strings as a consecutive substring. In order to analyze the average behavior of the optimal superstring length, substrings of specified lengths are considered with the letters selected independently at random. An asymptotic expression is obtained for the savings from compression, i.e. the difference between the uncompressed (concatenated) length and the optimal superstring length.