Special features of RAD Sequencing data:implications for genotyping

Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools

Community impacts of anthropogenic disturbance: natural enemies exploit multiple routes in pursuit of invading herbivore hosts

<p>Abstract</p> <p>Background</p> <p>Biological invasions provide a window on the process of community assembly. In particular, tracking natural enemy recruitment to invading hosts can reveal the relative roles of co-evolution (including local adaptation) and ecological sorting. We use molecular data to examine colonisation of northern Europe by the parasitoid <it>Megastigmus stigmatizans </it>following invasions of its herbivorous oak gallwasp hosts from the Balkans. Local host adaptation predicts that invading gallwasp populations will have been tracked primarily by sympatric Balkan populations of <it>M. stigmatizans </it>(Host Pursuit Hypothesis). Alternatively, ecological sorting allows parasitoid recruitment from geographically distinct populations with no recent experience of the invading hosts (Host Shift Hypothesis). Finally, we test for long-term persistence of parasitoids introduced via human trade of their hosts' galls (Introduction Hypothesis).</p> <p>Results</p> <p>Polymorphism diagnostic of different southern refugial regions was present in both mitochondrial and nuclear microsatellite markers, allowing us to identify the origins of northern European invaded range <it>M. stigmatizans </it>populations. As with their hosts, some invaded range populations showed genetic variation diagnostic of Balkan sources, supporting the Host Pursuit Hypothesis. In contrast, other invading populations had an Iberian origin, unlike their hosts in northern Europe, supporting the Host Shift Hypothesis. Finally, both British and Italian <it>M. stigmatizans </it>populations show signatures compatible with the Introduction Hypothesis from eastern Mediterranean sources.</p> <p>Conclusions</p> <p>These data reveal the continental scale of multi-trophic impacts of anthropogenic disturbance and highlight the fact that herbivores and their natural enemies may face very different constraints on range expansion. The ability of natural enemies to exploit ecologically-similar hosts with which they have had no historical association supports a major role for ecological sorting processes in the recent assembly of these communities. The multitude of origins of invading natural enemy populations in this study emphasises the diversity of mechanisms requiring consideration when predicting consequences of other biological invasions or biological control introductions.</p

Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319

The genome sequence of the human pathogen Corynebacterium diphtheriae bv. mitis strain ISS 3319 was determined and closed in this study. The genome is estimated to have 2,404,936 bp encoding 2,257 proteins. This strain also possesses a plasmid of 1,960 bp

Design and development of exome capture sequencing for the domestic pig (Sus scrofa)

Background: The domestic pig (Sus scrofa) is both an important livestock species and a model for biomedical research. Exome sequencing has accelerated identification of protein-coding variants underlying phenotypic traits in human and mouse. We aimed to develop and validate a similar resource for the pig.Results: We developed probe sets to capture pig exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs) and demonstrated proof-of-principle capture and sequencing of the pig exome in 96 pigs, encompassing 24 capture experiments. For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases. Bioinformatic analysis of the data revealed over 236,000 high confidence predicted SNPs and over 28,000 predicted indels.Conclusions: We have achieved coverage statistics similar to those seen with commercially available human and mouse exome kits. Exome capture in pigs provides a tool to identify coding region variation associated with production traits, including loss of function mutations which may explain embryonic and neonatal losses, and to improve genomic assemblies in the vicinity of protein coding genes in the pig

Seven Ulmus minor clones tolerant to Ophiostoma novo-ulmi registered as forest reproductive material in Spain

The Spanish elm programme began in 1986 in response to the devastating impact of Dutch elm disease on natural elm stands and urban trees. Its main objectives were to conserve remaining genetic resources and select and breed tolerant native elm genotypes. After 27 years of work conducting susceptibility trials on thousands of elm genotypes, the first seven tolerant Ulmus minor trees are now being registered by the Spanish Environmental Administration. This paper presents the results of the susceptibility tests on these clones and their distinctive genetic, morphological and phenological features. In all susceptibility trials the commercial “Sapporo Autumn Gold” clone, which is highly tolerant to O. novo-ulmi, was used as a control. The registered clones were named “Ademuz”, “Dehesa de la Villa”, “Majadahonda”, “Toledo”, “Dehesa de Amaniel”, “Retiro” and “Fuente Umbría”. The most tolerant clone was “Dehesa de Amaniel”, as its wilting values were below 5% during the two consecutive inoculation trials performed in Madrid. “Fuente Umbría”, tested over four consecutive years in Guadalajara and Palencia, was the Spanish clone with the most reliable tolerance level to O. novo-ulmi. The “Ademuz” and “Majadahonda” clones had the highest ornamental scores and are promising trees for use in urban environments and tree breeding for ornamental quality. These two genotypes showed a later bud burst phenology than the other U. minor clones, demonstrating suitability to areas with late frost events. The Spanish programme aims to substantially increase the range of tolerant native elms through new selections and crossings to gain a better understanding of the genetic basis of resistance

Prevalence and Persistence of Antibiotic Resistance Determinants in the Gut of Travelers Returning to the United Kingdom is Associated with Colonization by Pathogenic Escherichia coli

The gut microbiota constitutes an ideal environment for the selection, exchange, and carriage of antibiotic resistance determinants (ARDs), and international travel has been identified as a risk factor for acquisition of resistant organisms. Here, we present a longitudinal metagenomic analysis of the gut resistome in travellers to "high-risk"countries (Gutback). Fifty volunteers, recruited at a travel clinic in London, United Kingdom, provided stool samples before (pre-travel), immediately after (posttravel), and 6 months after their return (follow-up) from a high-risk destination. Fecal DNA was extracted, metagenomic sequencing performed and the resistome profiled. An increase in abundance and diversity of resistome was observed after travel. Significant increases in abundance were seen in antimicrobial genes conferring resistance to macrolides, third-generation cephalosporins, aminoglycosides, and sulfonamides. There was a significant association with increased resistome abundance if the participant experienced diarrhea during travel or took antibiotics, but these two variables were co-correlated. The resistome abundance returned to pre-travel levels by the 6-month sample point but there was evidence of persistence of several ARDs. The post-travel samples had an increase in abundance Escherichia coli which was positively associated with many acquired resistant determinants. Virulence and phylogenetic profiling revealed pathogenic E. coli significantly contributed to this increase abundance. In summary, in this study, foreign travel remains a significant risk factor for acquisition of microbes conferring resistance to multiple classes of antibiotics, often associated with symptomatic exposure to diarrhoeagenic E. coli

Genomic variation in macrophage-cultured European porcine reproductive and respiratory syndrome virus Olot/91 revealed using ultra-deep next generation sequencing

BACKGROUND: Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major economic impact worldwide. The etiologic agent of this disease is the PRRS virus (PRRSV). Increasing evidence suggest that microevolution within a coexisting quasispecies population can give rise to high sequence heterogeneity in PRRSV. FINDINGS: We developed a pipeline based on the ultra-deep next generation sequencing approach to first construct the complete genome of a European PRRSV, strain Olot/9, cultured on macrophages and then capture the rare variants representative of the mixed quasispecies population. Olot/91 differs from the reference Lelystad strain by about 5% and a total of 88 variants, with frequencies as low as 1%, were detected in the mixed population. These variants included 16 non-synonymous variants concentrated in the genes encoding structural and nonstructural proteins; including Glycoprotein 2a and 5. CONCLUSION: Using an ultra-deep sequencing methodology, the complete genome of Olot/91 was constructed without any prior knowledge of the sequence. Rare variants that constitute minor fractions of the heterogeneous PRRSV population could successfully be detected to allow further exploration of microevolutionary events

Ulmus laevis in the Iberian Peninsula: a review of its ecology and conservation

European white elm (Ulmus laevis Pallas) populations are scarce, small and fragmented in the Iberian Peninsula. Due to these characteristics the indigenous status of the species in the region has been questioned, whilst the species? role in Iberian riparian forest ecology has been neglected. Herein we review past studies regarding this species? distribution and ecology in the Iberian Peninsula, with special emphasis on the establishment of conservation priorities. We first present a collection of palaeogeographic, historic and genetic data suggesting that the Iberian Peninsula was a glacial refuge for U. laevis. Secondly, we analyse U. laevis distribution in relation to soil physico- chemical properties and water availability in Spain. Following this, we focus on the reproductive biology of the species, and investigate the effect of masting and empty seed production on predation and regeneration establishment. Finally, based on this knowledge, we propose conservation policies for U. laevis in the Iberian Peninsula

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p&lt;0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p&lt;0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised

Ormyrus nitidulus Fabricius 1804

8. Ormyrus nitidulus (Fabricius, 1804) Material examined: East-Azarbaijan, Arasbaran, ex Andricus curtisii (= mediterraneus), 1 Ψ. Same locality, ex A. quercustozae, 3 Ψ & 1 ɗ. Same locality, ex Cynips. quercusfolii on Quercus. macranthera, 1 ɗ. Kermanshah, Gahvareh, ex A. coriarius on Q. petraea, 1 Ψ. Same locality, ex Aphelonyx persica on Q. brantii, 3 Ψ. Same locality, 11 ɗ & 21 Ψ. Kordestan, Marivan, ex C. quercus, 6 Ψ & 7 ɗ. Same locality, ex Andricus askewi, 3 Ψ. Same locality, 11 Ψ & 12 ɗ. Same locality, ex A. galeatus, 6 Ψ & 1 ɗ. Same locality, ex A. lucidus, 1 Ψ. Same locality, ex A. mayri, 56 Ψ & 20 ɗ. Same locality, ex A. truncicolus, 1 ɗ. Lorestan, Ghalai, ii. 2003, ex Andricus curtisii on Q. infectoria, (E. Azizkhani), 2 Ψ & 1 ɗ. Same locality, 37 Ψ & 17 ɗ. Lorestan, Sar Pol Zahab, 1 Ψ. Lorestan, Javanrode, 6 Ψ & 1 ɗ. West-Azarbaijan, Piran-Shahr, ex A. caputmedusae, 1 Ψ. Same locality, A. polycerus, 6 Ψ. Same locality, ex A. pseudoaries on Q. petraea and Q. macranthera, 1 Ψ. West-Azarbaijan, Sar-Dasht, ex A. megalucidus, 1 Ψ. Same locality, ex A. sternlichti, 1 ɗ. Same locality, ex A. tomentosus, 1 Ψ. Same locality, ex Cynips divisa, 4 Ψ. Many specimens reared from a range of galls of Andricus, Aphelonyx and Cynips (Cynipidae) in the provinces of West-Azarbaijan, Lorestan, Kordestan and Kermanshah (Table 1). Exceptionally, Askew et al. (2006) mention an association of this species with the cynipid wasp Diplolepis rosae (L.) on Rosa. Ormyrus nitidulus is widely distributed in the West Palaearctic region (Noyes 2011) although it has not been mentioned for Middle East countries (Narendran et al. 2007). It is possible that the morphospecies O. nitidulus is a complex of cryptic species, as has been reported for other parasitoids of the oak gallwasp community (Nicholls et al. 2010). It displays a moderate amount of variation and molecular analysis reveals a number of clades, but we have not been able to completely match the molecular clades to morphological forms.Published as part of Lotfalizadeh, Hosseinali, Askew, Richard R., Fuentes-Utrilla, Pablo & I, Majid Tavak O L, 2012, The species of Ormyrus Westwood (Hymenoptera: Ormyridae) in Iran with description of an unusual new species, pp. 34-44 in Zootaxa 3300 on page 42, DOI: 10.5281/zenodo.21078