A draft genome sequence of the rose black spot fungus Diplocarpon rosae reveals a high degree of genome duplication

Background: Black spot is one of the most severe and damaging diseases of garden roses. We present the draft genome sequence of its causative agent Diplocarpon rosae as a working tool to generate molecular markers and to analyze functional and structural characteristics of this fungus. Results: The isolate DortE4 was sequenced with 191x coverage of different read types which were assembled into 2457 scaffolds. By evidence supported genome annotation with the MAKER pipeline 14,004 gene models were predicted and transcriptomic data indicated that 88.5% of them are expressed during the early stages of infection. Analyses of k-mer distributions resulted in unexpectedly large genome size estimations between 72.5 and 91.4 Mb, which cannot be attributed to its repeat structure and content of transposable elements alone, factors explaining such differences in other fungal genomes. In contrast, different lines of evidences demonstrate that a huge proportion (approximately 80%) of genes are duplicated, which might indicate a whole genome duplication event. By PCR-RFLP analysis of six paralogous gene pairs of BUSCO orthologs, which are expected to be single copy genes, we could show experimentally that the duplication is not due to technical error and that not all isolates tested possess all of the paralogs. Conclusions: The presented genome sequence is still a fragmented draft but contains almost the complete gene space. Therefore, it provides a useful working tool to study the interaction of D. rosae with the host and the influence of a genome duplication outside of the model yeast in the background of a phytopathogen

Mechanical forces due to lightning strikes to aircraft: a pseudo-stereo DIC technique for measuring full-field displacement

One of the major considerations currently affecting the design of composite aircraft structures is the damage resulting from lightning attachment. Full-field measurements of the displacement of materials under lightning attachment would provide a greater understanding of the forces induced by the high current waveform. Furthermore the understanding of the forces involved would allow for the validation of finite element models to simulate the effects of lightning attachment, therefore aiding in the design of solutions to reduce damage to aircraft structures. The study aimed to develop a pseudo-stereo high speed digital image correlation technique in order to obtain full-field information during lightning attachment based on a 100kA initial strike over a 500μs duration, the most severe waveform experienced. The technique that was developed gave full-field measurements for a 550x550x2mm 6082-T6 aluminium panel under a 100kA lightning attachment. Two correlation measurements were recorded at 3000 and 5000 frames per second. The displacement results are comparative with the theory of a cylindrical pressure expansion arising from the acoustic shockwave on attachment to the material. Further developments to this system could allow for more reliable results and higher frame rates which can be used to develop finite element simulations based on measured physical data

Gene duplication and protein evolution in tick-host interactions

Ticks modulate their hosts' defense responses by secreting a biopharmacopiea of hundreds to thousands of proteins and bioactive chemicals into the feeding site (tick-host interface). These molecules and their functions evolved over millions of years as ticks adapted to blood-feeding, tick lineages diverged, and host-shifts occurred. The evolution of new proteins with new functions is mainly dependent on gene duplication events. Central questions around this are the rates of gene duplication, when they occurred and how new functions evolve after gene duplication. The current review investigates these questions in the light of tick biology and considers the possibilities of ancient genome duplication, lineage specific expansion events, and the role that positive selection played in the evolution of tick protein function. It contrasts current views in tick biology regarding adaptive evolution with the more general view that neutral evolution may account for the majority of biological innovations observed in ticks.The Economic Competitive Support Programme (30/01/V010) and the National Research Foundation (NRF) Incentive Funding (IFR2011032400016) for Rated Researchers (NRF-Mans). MdC was supported by an NRF/Department of Science and Technology—Professional Development Program (NRF/DST-PDP) studentship.http://www.frontiersin.org/Cellular_and_Infection_Microbiologyam2017Veterinary Tropical Disease

Draft genomes of two Artocarpus plants, jackfruit (A. heterophyllus) and breadfruit (A. altilis)

Two of the most economically important plants in the Artocarpus genus are jackfruit (A. heterophyllus Lam.) and breadfruit (A. altilis (Parkinson) Fosberg). Both species are long-lived trees that have been cultivated for thousands of years in their native regions. Today they are grown throughout tropical to subtropical areas as an important source of starch and other valuable nutrients. There are hundreds of breadfruit varieties that are native to Oceania, of which the most commonly distributed types are seedless triploids. Jackfruit is likely native to the Western Ghats of India and produces one of the largest tree-borne fruit structures (reaching up to 45 kg). To-date, there is limited genomic information for these two economically important species. Here, we generated 273 Gb and 227 Gb of raw data from jackfruit and breadfruit, respectively. The high-quality reads from jackfruit were assembled into 162,440 scaffolds totaling 982 Mb with 35,858 genes. Similarly, the breadfruit reads were assembled into 180,971 scaffolds totaling 833 Mb with 34,010 genes. A total of 2822 and 2034 expanded gene families were found in jackfruit and breadfruit, respectively, enriched in pathways including starch and sucrose metabolism, photosynthesis, and others. The copy number of several starch synthesis-related genes were found to be increased in jackfruit and breadfruit compared to closely-related species, and the tissue-specific expression might imply their sugar-rich and starch-rich characteristics. Overall, the publication of high-quality genomes for jackfruit and breadfruit provides information about their specific composition and the underlying genes involved in sugar and starch metabolism

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Cooperation and conflict in cancer: An evolutionary perspective

Evolutionary approaches to carcinogenesis have gained prominence in the literature and enhanced our understanding of cancer. However, an appreciation of neoplasia in the context of evolutionary transitions, particularly the transition from independent genes to a fullyintegrated genome, is largely absent. In the gene–genome evolutionary transition, mobile genetic elements (MGEs) can be studied as the extant exemplars of selfish autonomous lowerlevel units that cooperated to form a higher-level, functionally integrated genome. Here,we discuss levels of selection in cancer cells. In particular, we examine the tension between gene and genome units of selection by examining the expression profiles of MGE domains in an array of human cancers. Overall, across diverse cancers, there is an aberrant expression of several families of mobile elements, including the most common MGE in the human genome, retrotransposon LINE 1. These results indicate an alternative life-history strategy for MGEs in the cancers studied. Whether the aberrant expression is the cause or effect oftumourigenesis is unknown, although some evidence suggests that dysregulation of MGEs can play a role in cancer origin and progression. These data are interpreted in combination with phylostratigraphic reports correlating the origin of cancer genes with multicellularity and other potential increases in complexity in cancer cell populations. Cooperation and conflict between individuals at the gene, genome and cell level provide an evolutionary medicineperspective of cancer that enhances our understanding of disease pathogenesis and treatment