138 research outputs found
Conserving coffee genetic resources : complementary strategies for ex situ conservation of coffee (Coffea arabica L.) genetic resources : a case study in CATIE, Costa Rica
Identification of the First Oomycete Mating-type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara viticola
Mating types are self-incompatibility systems that promote outcrossing in plants, fungi, and oomycetes. Mating-type genes have been widely studied in plants and fungi but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570-kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Functional studies will, however, be required to validate the function of these genes and find the actual determinants of mating type. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions
A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94âMb assembly with high contiguity (359 scaffolds for a N50 of 706.5âkb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plantâpathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species
Abortive intermediates in transcription by wheat-germ RNA polymerase II. Dynamic aspects of enzyme/template interactions in selection of the enzyme synthetic mode
Cellular Array Morphology During Directional Solidification
Cellular array morphology has been examined in the shallow cell, deep cell, and cell-to-dendrite transition regime in Pb-2.2 wt pct Sb and Al-4.1 wt pct Cu alloy single-crystal samples that were directionally solidified along [100]. Statistical analysis of the cellular spacing distribution on transverse sections has been carried out using minimum spanning tree (MST), Voronoi polygons, radial distribution factor, and fast Fourier transform (FFT) techniques. The frequency distribution of the number of nearest neighbors and the MST parameters suggest that the arrangement of cells may be visualized as a hexagonal tessellation with superimposed 50 pct random noise. However, the power spectrum of the Fourier transform of the cell centers shows a diffused single-ring pattern that does not agree with the power spectrum from the hexagonal tessellation having a 50 pct superimposed random (uniformly distributed or Gaussian) noise. The radial distribution factor obtained from the cells is similar to that of liquids. An overall steady-state distribution in terms of the mean primary spacing is achieved after directional solidification of about three mushy-zone lengths. However, the process of nearest-neighbor interaction continues throughout directional solidification, as indicated by about 14 pct of the cells undergoing submerging in the shallow cell regime or by an increasing first and second nearest-neighbor ordering along the growth direction for the cells at the cell-to-dendrite transition. The nature of cell distribution in the Al-Cu alloy appears to be the same as that in the Pb-Sb. The ratio between the upper and lower limits of the primary spacing, as defined by the largest and the smallest 10 pct of the population, respectively, is constant: 1.43 +/- 0.11. It does not depend upon the solidification processing conditions
Interactions between Kluyveromyces marxianus from cheese origin and the intestinal symbiont Bacteroides thetaiotaomicron: Impressive antioxidative effects
The effects of yeast Kluyveromyces marxianus S-2-05, of cheese origin, were assessed on the intestine anaerobe symbiont Bacteroides thetaiotaomicron ATCC 29741 to unveil any changes in its antioxidant properties. To this end, these microorganisms were grown and incubated either separately, or co-incubated, under anaerobic atmosphere. Afterwards, the microbial cells were recovered and washed, and extracts were prepared using a sterile detergent solution to mimic the intestine detergent content. The extracts prepared from K. marxianus S-2-05 and reference strain K. marxianus MUCL 29917, grown under different conditions, were assessed for their antioxidant properties against superoxide anion and hydrogen peroxide. Extracts from both yeasts showed antioxidative effects, which were particularly important for K. marxianus S-02-5 after anaerobic incubation. Moreover, K. marxianus S-02-5 displayed a high level of activity against the aforementioned reactive oxygen species, enhancing that of B. thetaiotaomicron ATCC 29741, after the co-incubation process. Two-dimensional polyacrylamide gel electrophoresis was used to separate the proteins extracted. Superoxide dismutase, thiol peroxidase, rubrerythrin -intensively produced by B. thetaiotaomicron induced by the yeast-were identified by mass spectrometry. The antioxidative potential evidenced for K. marxianus S-02-5 is another advantage which could justify the utilization of this strain as a probiotic for countering intestinal inflammatory processes. © 2017 Elsevier Lt
Primary Dendrite Distribution and Disorder During Directional Solidification of Pb-Sb Alloys
Pb-2.2 wt pct Sb and Pb-5.8 wt pet Sb alloys have been directionally solidified from a single-crystal seed with its [100] orientation parallel to the growth direction, to examine the primary dendrite distribution and disorder of the dendrite arrays. The dendrite distribution and ordering have been investigated using analysis techniques such as the Gauss-amplitude fit to the frequency distribution of nearest and higher-order spacings, minimum spanning tree (MST), Voronoi polygon, and Fourier transform (FT) of the dendrite centers. Since the arrangement of dendrites is driven by the requirement to accommodate side-branch growth along the (100) directions, the FT images of the fully developed dendrite centers contain spots which indicate this preferred alignment. A directional solidification distance of about three mushy-zone lengths is sufficient to ensure a steady-state dendritic array, in terms of reaching a constant mean primary spacing. However, local dendrite ordering continues throughout the directional solidification process. The interdendritic convection not only decreases the mean primary spacing, it also makes the dendrite array more disordered and reduces the ratio of the upper and lower spacing limits, as defined by the largest 5 pct and the smallest 5 pct of the population
Comparative Transcriptome Analysis of Three Oil Palm Fruit and Seed Tissues That Differ in Oil Content and Fatty Acid Composition
The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits
Background: Understanding the genetic elements that contribute to key aspects of coffee biology will have an impact on future agronomical improvements for this economically important tree. During the past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results: The "PUCE CAFE" Project, organized by the scientific consortium NESTLE/IRD/CIRAD, has developed an oligo-based microarray using 15,721 unigenes derived from published coffee EST sequences mostly obtained from different stages of fruit development and leaves in Coffea Canephora (Robusta). Hybridizations for two independent experiments served to compare global gene expression profiles in three types of tissue matter (mature beans, leaves and flowers) in C. canephora as well as in the leaves of three different coffee species (C. canephora, C. eugenoides and C. arabica). Microarray construction, statistical analyses and validation by Q-PCR analysis are presented in this study. Conclusion: We have generated the first 15 K coffee array during this PUCE CAFE project, granted by Genoplante (the French consortium for plant genomics). This new tool will help study functional genomics in a wide range of experiments on various plant tissues, such as analyzing bean maturation or resistance to pathogens or drought. Furthermore, the use of this array has proven to be valid in different coffee species (diploid or tetraploid), drastically enlarging its impact for high-throughput gene expression in the community of coffee research
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