Investigating hookworm genomes by comparative analysis of two Ancylostoma species

Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans. Applying genomics techniques to these species, we analyzed 3,840 and 3,149 genes from Ancylostoma caninum and A. ceylanicum. Results Transcripts originated from libraries representing infective L3 larva, stimulated L3, arrested L3, and adults. Most genes are represented in single stages including abundant transcripts like hsp-20 in infective L3 and vit-3 in adults. Over 80% of the genes have homologs in C. elegans, and nearly 30% of these were with observable RNA interference phenotypes. Homologies were identified to nematode-specific and clade V specific gene families. To study the evolution of hookworm genes, 574 A. caninum / A. ceylanicum orthologs were identified, all of which were found to be under purifying selection with distribution ratios of nonsynonymous to synonymous amino acid substitutions similar to that reported for C. elegans / C. briggsae orthologs. The phylogenetic distance between A. caninum and A. ceylanicum is almost identical to that for C. elegans / C. briggsae. Conclusion The genes discovered should substantially accelerate research toward better understanding of the parasites' basic biology as well as new therapies including vaccines and novel anthelmintics

Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option availabl

Innovation and constraint leading to complex multicellularity in the Ascomycota

10.1038/ncomms14444Nature Communications81444

Shed Light in the DaRk LineagES of the Fungal Tree of Life-STRES

Contains fulltext : 228731.pdf (publisher's version ) (Open Access

Diagen: A Model-driven Framework for Integrating Bioinformatic Tools

Abstract. Nowadays, the diagnosis of disease based on genomic information is feasible by searching genetic variations on DNA sequences. However, geneticists struggle with bioinformatic tools that are supposed to simplify DNA sequence analysis. As a universal tool to support every requirement is far from be implemented, geneticists themselves must solve the data exchange among several tools. Due to the fact that there are no standards to support this integration task, it must be managed in every analysis. This paper proposes addressing this integration by means of a model-driven framework. The Diagen framework is a software implementation based on conceptual modeling principles that formalizes data exchange and simpli es bioinformatic tool integration. First, we analyze how conceptual modeling can be used to deal with data exchange among tools. And then, as a proof of concept, the presented framework is used to search for variations on the BRCA2 gene using real DNA samples and a set of speci c bioinformatic tools. Keywords: Model-Driven Development, Tool Integration, DNA sequence analysi

Complete genome sequence of a Staphylococcus aureus sequence type 612 isolate from an Australian Horse

© 2018 Murphy et al. Staphylococcus aureus is a serious pathogen of humans and animals. Multilocus sequence type 612 is dominant and highly virulent in South African hospitals but relatively uncommon elsewhere. We present the complete genome sequence of methicillin-resistant Staphylococcus aureus strain SVH7513, isolated from a horse at a veterinary clinic in New South Wales, Australia

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis.

Pneumocystis species are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivable in vitro Human Pneumocystis infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of Pneumocystis infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate that Pneumocystis species diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation of Pneumocystis populations during their spread across mammals.IMPORTANCE Understanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology. Pneumocystis, a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans, Pneumocystis can cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of different Pneumocystis species infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest that Pneumocystis may have undergone recent host shifts. The results demonstrate that Pneumocystis strains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens

Scientific Workflows: Business as Usual

Abstract. Business workflow management and business process modeling are mature research areas, whose roots go far back to the early days of office automation systems. Scientific workflow management, on the other hand, is a much more recent phenomenon, triggered by (i) a shift towards data-intensive and computational methods in the natural sciences, and (ii) the resulting need for tools that can simplify and automate recurring computational tasks. In this paper, we provide an introduction and overview of scientific workflows, highlighting features and important concepts commonly found in scientific workflow applications. We illustrate these using simple workflow examples from a bioinformatics domain. We then discuss similarities and, more importantly, differences between scientific workflows and business workflows. While some concepts and solutions developed in one domain may be readily applicable to the other, there remain sufficiently many differences that warrant a new research effort at the intersection of scientific and business workflows. We close by proposing a number of research opportunities for cross-fertilization between the scientific workflow and business workflow communities.

The 2006 NESCent phyloinformatics hackathon: A field report

10.1177/117693430700300016Evolutionary Bioinformatics3287-29