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

Frontières des hommes et échanges des plantes cultivées

Une analyse comparative de la relation entre diversités ethnolinguistique et génétique a été menée dans le bassin du lac Tchad sur les variétés de trois espèces : le mil, le sorgho et le pois de terre. Pour le mil, très allogame, les résultats conduisent à proposer l’hypothèse d’une coïncidence entre la distribution des groupes génétiques et celles de groupes ethnolinguistiques. Ainsi, des « barrières » sociales à la diffusion des échanges de variétés révélées par les enquêtes anthropologiques, limitent les flux de gènes. La répartition de la diversité génétique du pois de terre, autogame et de culture souvent marginale, révèle une histoire riche en échanges et circulations des semences, en accord avec un système de dénomination largement partagé par toutes les communautés, et une circulation marchande importante. Le sorgho, préférentiellement autogame, pour lequel les emprunts de variétés sont fréquents, révèle une situation intermédiaire. Les groupes génétiques ont une répartition fragmentée, la sélection pour la conservation de types nommés et le système de reproduction majoritairement autogame limitant les échanges génétiques entre ces groupes.A comparative analysis of the relationships between ethno-linguistic and genetic diversities has been carried out in the Lake Chad basin, on pearl millet, sorghum and Bambara groundnut varieties. Results suggest the hypothesis of a coincidence in spatial distribution of farmers social groups and pearl millet genetic groups, despite its outcrossing mating system. The ethnographic surveys indicate ethnic barriers that reduce exchanges of varieties and gene flow. The Bambara groundnut, a self-pollinated species, is mainly a marginal crop. Its genetic diversity witnesses important seed exchanges that probably occurred throughout the history of the cultivation of this plant in this region. This result is in agreement with both the similar naming systems in the different ethnic groups and the important merchant exchanges of this crop. For sorghum, use and adoption of exotic varieties are frequent, which could contribute to explain the patchy spatial distribution of genetic groups. However, farmer’s selection for the conservation of well-identified varieties and a mainly selfing mating system, contribute to limit gene flow between varieties

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 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) 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 plant–pathogen 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

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

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

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

An integrated bioinformatics analysis reveals divergent evolutionary pattern of oil biosynthesis in high- and low-oil plants

Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content