An efficient approach to BAC based assembly of complex genomes

Background: There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate ‘gold’ reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. Results: We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. Conclusions: We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes

Exploring the utility of cross-laboratory RAD-sequencing datasets for phylogenetic analysis

BACKGROUND: Restriction site-Associated DNA sequencing (RAD-Seq) is widely applied to generate genome-wide sequence and genetic marker datasets. RAD-Seq has been extensively utilised, both at the population level and across species, for example in the construction of phylogenetic trees. However, the consistency of RAD-Seq data generated in different laboratories, and the potential use of cross-species orthologous RAD loci in the estimation of genetic relationships, have not been widely investigated. This study describes the use of SbfI RAD-Seq data for the estimation of evolutionary relationships amongst ten teleost fish species, using previously established phylogeny as a benchmark. RESULTS: The number of orthologous SbfI RAD loci identified decreased with increasing evolutionary distance between the species, with several thousand loci conserved across five salmonid species (divergence ~50 MY), and several hundred conserved across the more distantly related teleost species (divergence ~100–360 MY). The majority (>70%) of loci identified between the more distantly related species were genic in origin, suggesting that the bias of SbfI towards genic regions is useful for identifying distant orthologs. Interspecific single nucleotide variants at each orthologous RAD locus were identified. Evolutionary relationships estimated using concatenated sequences of interspecific variants were congruent with previously published phylogenies, even for distantly (divergence up to ~360 MY) related species. CONCLUSION: Overall, this study has demonstrated that orthologous SbfI RAD loci can be identified across closely and distantly related species. This has positive implications for the repeatability of SbfI RAD-Seq and its potential to address research questions beyond the scope of the original studies. Furthermore, the concordance in tree topologies and relationships estimated in this study with published teleost phylogenies suggests that similar meta-datasets could be utilised in the prediction of evolutionary relationships across populations and species with readily available RAD-Seq datasets, but for which relationships remain uncharacterised. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-015-1261-2) contains supplementary material, which is available to authorized users

Improving Access to Mental Health Care in an Orthodox Jewish Community: A Critical Reflection Upon the Accommodation of Otherness

The English National Health Service (NHS) has significantly extended the supply of evidence based psychological interventions in primary care for people experiencing common mental health problems. Yet despite the extra resources, the accessibility of services for ‘under-served’ ethnic and religious minority groups, is considerably short of the levels of access that may be necessary to offset the health inequalities created by their different exposure to services, resulting in negative health outcomes. This paper offers a critical reflection upon an initiative that sought to improve access to an NHS funded primary care mental health service to one ‘under-served’ population, an Orthodox Jewish community in the North West of England

The phenomenology and ontology of the Oedipus complex

Abstract This paper will continue my earlier work that provided a phenomenological and ontological explanation of Jung’s complex theory (Gildersleeve in Procedia Soc Behav Sci 217:967–976, 2016). This paper will contribute to that earlier work by providing a phenomenological explanation of Freud’s writing on the Oedipus complex and this phenomenological description will also allow the ontological meaning of the Oedipus complex to be understood. This work reveals the convergent ideas between Martin Heidegger’s philosophy and Sigmund Freud’s psychoanalysis and this provides support to defend the existence of Freud’s arguments on the Oedipus complex by explaining it through the lived experience vocabulary of phenomenology. This article also demonstrates that Jung’s and Freud’s writing on complexes possess the same phenomenological and ontological structure and this shows that their respective theories can be integrated to develop psychoanalytic theory and practice in new ways. Finally, this work contributes to the writing of Medard Boss and the Daseinsanalysis literature that has yet to provide a Daseinsanalytic interpretation of the Oedipus complex