Genome-enabled phylogeographic investigation of the quarantine pathogen Ralstonia solanacearum race 3 biovar 2 and screening for sources of resistance against its core effectors.

Phylogeographic studies inform about routes of pathogen dissemination and are instrumental for improving import/export controls. Genomes of seventeen isolates of the bacterial wilt and potato brown rot pathogen Ralstonia solanacearum race 3 biovar 2 (R3bv2), a select agent in the USA, were thus analyzed to get insight into the phylogeography of this pathogen. Thirteen of fourteen isolates from Europe, Africa, and Asia were found to belong to a single clonal lineage while isolates from South America were genetically diverse and carried ancestral alleles at the analyzed genomic loci consistent with a South American origin of R3bv2. The R3bv2 isolates share a core repertoire of thirty-one type III-secreted effector genes representing excellent candidates to be targeted with resistance genes in breeding programs to develop durable disease resistance. Towards this goal, 27 R3bv2 effectors were tested in eggplant, tomato, pepper, tobacco, and lettuce for induction of a hypersensitive-like response indicative of recognition by cognate resistance receptors. Fifteen effectors, eight of them core effectors, triggered a response in one or more plant species. These genotypes may harbor resistance genes that could be identified and mapped, cloned and expressed in tomato or potato, for which sources of genetic resistance to R3bv2 are extremely limited.National Science Foundatio

Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant

© Gramazio et al.; licensee BioMed Central. 2014. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated

Crop wild relatives of the brinjal eggplant ( Solanum melongena ): Poorly represented in genebanks and many species at risk of extinction

This is the publisher's Early View pdf without final pagination .© 2016 Botanical Society of America. This is an open access article, available to all readers online, published under a creative commons license. The attached file is the published version of the article

Triton Haze Analogs: The Role of Carbon Monoxide in Haze Formation

Triton is the largest moon of the Neptune system and possesses a thin nitrogen atmosphere with trace amounts of carbon monoxide and methane, making it of similar composition to that of the dwarf planet Pluto. Like Pluto and Saturn\u27s moon Titan, Triton has a haze layer thought to be composed of organics formed through photochemistry. Here, we perform atmospheric chamber experiments of 0.5% CO and 0.2% CH4 in N2 at 90 K and 1 mbar to generate Triton haze analogs. We then characterize the physical and chemical properties of these particles. We measure their production rate, their bulk composition with combustion analysis, their molecular composition with very high resolution mass spectrometry, and their transmission and reflectance from the optical to the near-infrared with Fourier Transform Infrared (FTIR) Spectroscopy. We compare these properties to existing measurements of Triton\u27s tenuous atmosphere and surface, as well as contextualize these results in view of all the small, hazy, nitrogen-rich worlds of our solar system. We find that carbon monoxide present at greater mixing ratios than methane in the atmosphere can lead to significantly oxygen- and nitrogen-rich haze materials. These Triton haze analogs have clear observable signatures in their near-infrared spectra, which may help us differentiate the mechanisms behind haze formation processes across diverse solar system bodies

Identification of Type 1 Diabetes-Associated DNA Methylation Variable Positions That Precede Disease Diagnosis

Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is similar to 50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. We generated genome-wide DNA methylation profiles of purified CD14(+) monocytes (an immune effector cell type relevant to T1D pathogenesis) from 15 T1D-discordant MZ twin pairs. This identified 132 different CpG sites at which the direction of the intra-MZ pair DNA methylation difference significantly correlated with the diabetic state, i.e. T1D-associated methylation variable positions (T1D-MVPs). We confirmed these T1D-MVPs display statistically significant intra-MZ pair DNA methylation differences in the expected direction in an independent set of T1D-discordant MZ pairs (P = 0.035). Then, to establish the temporal origins of the T1D-MVPs, we generated two further genome-wide datasets and established that, when compared with controls, T1D-MVPs are enriched in singletons both before (P = 0.001) and at (P = 0.015) disease diagnosis, and also in singletons positive for diabetes-associated autoantibodies but disease-free even after 12 years follow-up (P = 0.0023). Combined, these results suggest that T1D-MVPs arise very early in the etiological process that leads to overt T1D. Our EWAS of T1D represents an important contribution toward understanding the etiological role of epigenetic variation in type 1 diabetes, and it is also the first systematic analysis of the temporal origins of disease-associated epigenetic variation for any human complex disease

Elephant Moraine 96029, a very mildly aqueously altered and heated CM carbonaceous chondrite: Implications for the drivers of parent body processing

Elephant Moraine (EET) 96029 is a CMcarbonaceous chondrite regolith breccia with evidence for unusually mild aqueous alteration, a later phase of heating and terrestrial weathering. The presence of phyllosilicates and carbonates within chondrules and the fine-grained matrix indicates that this meteorite was aqueously altered in its parent body. Features showing that water-mediated processing was arrested at a very early stage include a matrix with a low magnesium/iron ratio, chondrules whose mesostasis contains glass and/or quench crystallites, and a gehlenite-bearing calcium- and aluminium-rich inclusion. EET 96029 is also rich in Fe,Ni metal relative to other CM chondrites, and more was present prior to its partial replacement by goethite during Antarctic weathering. In combination, these properties indicate that EET 96029 is one of the least aqueously altered CMs yet described (CM2.7) and so provides new insights into the original composition of its parent body. Following aqueous alteration, and whilst still in the parent body regolith, the meteorite was heated to ~400–600 °C by impacts or solar radiation. Heating led to the amorphisation and dehydroxylation of serpentine, replacement of tochilinite by magnetite, loss of sulphur from the matrix, and modification to the structure of organic matter that includes organic nanoglobules. Significant differences between samples in oxygen isotope compositions, and water/hydroxyl contents, suggests that the meteorite contains lithologies that have undergone different intensities of heating. EET 96029 may be more representative of the true nature of parent body regoliths than many other CM meteorites, and as such can help interpret results from the forthcoming missions to study and return samples from C-complex asteroids

Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

[EN] Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.This work has been funded in part by European Unions Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Funding has also been received from the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. This last project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website:http://www.cwrdiversity.org/. Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Santiago Grisolia Programme (FCJI-2015-24835). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Acquadro, A.; Barchi, L.; Gramazio, P.; Portis, E.; Vilanova Navarro, S.; Comino, C.; Plazas Ávila, MDLO.... (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS ONE. 12(7). https://doi.org/10.1371/journal.pone.0180774Se018077412

Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

[EN] Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers are amongst the most common markers of choice for studies of diversity and relationships in horticultural species. We have used 11 SSR and 35 SNP markers derived from transcriptome sequencing projects to fingerprint 48 accessions of a collection of brinjal (Solanum melongena), gboma (S. macrocarpon) and scarlet (S. aethiopicum) eggplant complexes, which also include their respective wild relatives S. incanum, S. dasyphyllum and S. anguivi. All SSR and SNP markers were polymorphic and 34 and 36 different genetic fingerprints were obtained with SSRs and SNPs, respectively. When combining both markers all accessions but two had different genetic profiles. Although on average SSRs were more informative than SNPs, with a higher number of alleles, genotypes and polymorphic information content (PIC), and expected heterozygosity (He) values, SNPs have proved highly informative in our materials. Low observed heterozygosity (Ho) and high fixation index (f) values confirm the high degree of homozygosity of eggplants. Genetic identities within groups of each complex were higher than with groups of other complexes, although differences in the ranks of genetic identity values among groups were observed between SSR and SNP markers. For low and intermediate values of pair-wise SNP genetic distances, a moderate correlation between SSR and SNP genetic distances was observed (r(2) = 0.592), but for high SNP genetic distances the correlation was low (r(2) = 0.080). The differences among markers resulted in different phenogram topologies, with a different eggplant complex being basal (gboma eggplant for SSRs and brinjal eggplant for SNPs) to the two others. Overall the results reveal that both types of markers are complementary for eggplant fingerprinting and that interpretation of relationships among groups may be greatly affected by the type of marker used.This work has been funded by European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia y Competitividad and Fondo Europeo de Desarrollo Regional (Grant AGL2015-64755-R from MINECO/FEDER). Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral contract (Programa FPI de la UPV-Subprograma 1/2013 call). Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Juan de la Cierva-Formacion programme (FJCI-2015-24835).Gramazio, P.; Prohens Tomás, J.; Borras, D.; Plazas Ávila, MDLO.; Herraiz García, FJ.; Vilanova Navarro, S. 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Characterising the CI and CI-like carbonaceous chondrites using thermogravimetric analysis and infrared spectroscopy

The CI and CI-like chondrites provide a record of aqueous alteration in the early solar system. However, the CI-like chondrites differ in having also experienced a late stage period of thermal metamorphism. In order to constrain the nature and extent of the aqueous and thermal alteration, we have investigated the bulk mineralogy and abundance of H2O in the CI and CI-like chondrites using thermogravimetric analysis and infrared spectroscopy. The CI chondrites Ivuna and Orgueil show significant mass loss (28.5–31.8 wt.%) upon heating to 1000 °C due to dehydration and dehydroxylation of abundant phyllosilicates and Fe-(oxy)hydroxides and the decomposition of Fe-sulphides, carbonates and organics. Infrared spectra for Ivuna and Orgueil have a prominent 3-μm feature due to bound −OH/H2O in phyllosilicates and Fe-(oxy)hydroxides and only a minor 11-μm feature from anhydrous silicates. These characteristics are consistent with previous studies indicating that the CI chondrites underwent near-complete aqueous alteration. Similarities in the total abundance of H2O and 3 μm/11 μm ratio suggest that there is no difference in the relative degree of hydration experienced by Ivuna and Orgueil. In contrast, the CI-like chondrites Y-82162 and Y-980115 show lower mass loss (13.8–18.8 wt.%) and contain >50 % less H2O than the CI chondrites. The 3-μm feature is almost absent from spectra of Y-82162 and Y-980115 but the 11-μm feature is intense. The CI-like chondrites experienced thermal metamorphism at temperatures >500 °C that initially caused dehydration and dehydroxylation of phyllosilicates before partial recrystallization back into anhydrous silicates. The surfaces of many C-type asteroids were probably heated through impact metamorphism and/or solar radiation, so thermally altered carbonaceous chondrites are likely good analogues for samples that will be returned by the Hayabusa-2 and OSIRIS-REx missions