Patterns of Sequence Divergence and Evolution of the S1 Orthologous Regions between Asian and African Cultivated Rice Species

A strong postzygotic reproductive barrier separates the recently diverged Asian and African cultivated rice species, Oryza sativa and O. glaberrima. Recently a model of genetic incompatibilities between three adjacent loci: S1A, S1 and S1B (called together the S1 regions) interacting epistatically, was postulated to cause the allelic elimination of female gametes in interspecific hybrids. Two candidate factors for the S1 locus (including a putative F-box gene) were proposed, but candidates for S1A and S1B remained undetermined. Here, to better understand the basis of the evolution of regions involved in reproductive isolation, we studied the genic and structural changes accumulated in the S1 regions between orthologous sequences. First, we established an 813 kb genomic sequence in O. glaberrima, covering completely the S1A, S1 and the majority of the S1B regions, and compared it with the orthologous regions of O. sativa. An overall strong structural conservation was observed, with the exception of three isolated regions of disturbed collinearity: (1) a local invasion of transposable elements around a putative F-box gene within S1, (2) the multiple duplication and subsequent divergence of the same F-box gene within S1A, (3) an interspecific chromosomal inversion in S1B, which restricts recombination in our O. sativa×O. glaberrima crosses. Beside these few structural variations, a uniform conservative pattern of coding sequence divergence was found all along the S1 regions. Hence, the S1 regions have undergone no drastic variation in their recent divergence and evolution between O. sativa and O. glaberrima, suggesting that a small accumulation of genic changes, following a Bateson-Dobzhansky-Muller (BDM) model, might be involved in the establishment of the sterility barrier. In this context, genetic incompatibilities involving the duplicated F-box genes as putative candidates, and a possible strengthening step involving the chromosomal inversion might participate to the reproductive barrier between Asian and African rice species

An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research

<p>Abstract</p> <p>Background</p> <p>Nocturnal insects such as moths are ideal models to study the molecular bases of olfaction that they use, among examples, for the detection of mating partners and host plants. Knowing how an odour generates a neuronal signal in insect antennae is crucial for understanding the physiological bases of olfaction, and also could lead to the identification of original targets for the development of olfactory-based control strategies against herbivorous moth pests. Here, we describe an Expressed Sequence Tag (EST) project to characterize the antennal transcriptome of the noctuid pest model, <it>Spodoptera littoralis</it>, and to identify candidate genes involved in odour/pheromone detection.</p> <p>Results</p> <p>By targeting cDNAs from male antennae, we biased gene discovery towards genes potentially involved in male olfaction, including pheromone reception. A total of 20760 ESTs were obtained from a normalized library and were assembled in 9033 unigenes. 6530 were annotated based on BLAST analyses and gene prediction software identified 6738 ORFs. The unigenes were compared to the <it>Bombyx mori </it>proteome and to ESTs derived from Lepidoptera transcriptome projects. We identified a large number of candidate genes involved in odour and pheromone detection and turnover, including 31 candidate chemosensory receptor genes, but also genes potentially involved in olfactory modulation.</p> <p>Conclusions</p> <p>Our project has generated a large collection of antennal transcripts from a Lepidoptera. The normalization process, allowing enrichment in low abundant genes, proved to be particularly relevant to identify chemosensory receptors in a species for which no genomic data are available. Our results also suggest that olfactory modulation can take place at the level of the antennae itself. These EST resources will be invaluable for exploring the mechanisms of olfaction and pheromone detection in <it>S. littoralis</it>, and for ultimately identifying original targets to fight against moth herbivorous pests.</p

MetaPDOcheese : investigation of the drivers of microbial communities from French PDO milks and cheeses

International audienceProtected Designation of Origin (PDO) cheeses are generally considered as high quality, non-standardised fermented products whose sensory richness arises from a variety of milk production and processing conditions. These practices would contribute to shaping microbial communities that have adapted to the dairy environment. In this most comprehensive study ever conducted on French PDO cheeses, our objective was to characterise the drivers of microbial communities in milks and the associated cheeses, and their relationships to biogeography, herd management and cheese processing practices. Thanks to the contribution of PDO cheese stakeholders, we sampled 1,145 PDO cheeses (each for rind and core) and 390 milks covering the diversity of the 44 French ripened PDO cheeses and collected detailed data on their production conditions. We characterised the bacterial and fungal communities of milks and cheeses using 16S rRNA and ITS2 gene sequencing. A total of 1,230 bacterial species and 1,367 fungal species were identified from the milk samples, with variations according to the dairy species. A total of 820 bacterial species and 333 fungal species were identified in cheeses. The core microbiome in cheese was limited to one fungal species (Geotrichum candidum) at 100% prevalence. The cheese’s microbiota differed in terms of richness and composition between the seven cheese families and within families, according to PDO labels. Secondary structuring factors, as the dairy species, the geographical area and cheese ripening practices, were also highlighted across cheese families, demonstrating a contribution of biogeography and PDO-specific know-how in shaping the cheese microbiota

MetaPDOcheese : investigation of the drivers of microbial communities from French PDO milks and cheeses

International audienceProtected Designation of Origin (PDO) cheeses are generally considered as high quality, non-standardised fermented products whose sensory richness arises from a variety of milk production and processing conditions. These practices would contribute to shaping microbial communities that have adapted to the dairy environment. In this most comprehensive study ever conducted on French PDO cheeses, our objective was to characterise the drivers of microbial communities in milks and the associated cheeses, and their relationships to biogeography, herd management and cheese processing practices. Thanks to the contribution of PDO cheese stakeholders, we sampled 1,145 PDO cheeses (each for rind and core) and 390 milks covering the diversity of the 44 French ripened PDO cheeses and collected detailed data on their production conditions. We characterised the bacterial and fungal communities of milks and cheeses using 16S rRNA and ITS2 gene sequencing. A total of 1,230 bacterial species and 1,367 fungal species were identified from the milk samples, with variations according to the dairy species. A total of 820 bacterial species and 333 fungal species were identified in cheeses. The core microbiome in cheese was limited to one fungal species (Geotrichum candidum) at 100% prevalence. The cheese’s microbiota differed in terms of richness and composition between the seven cheese families and within families, according to PDO labels. Secondary structuring factors, as the dairy species, the geographical area and cheese ripening practices, were also highlighted across cheese families, demonstrating a contribution of biogeography and PDO-specific know-how in shaping the cheese microbiota

MetaPDOcheese : investigation of the drivers of microbial communities from French PDO milks and cheeses

International audienceProtected Designation of Origin (PDO) cheeses are generally considered as high quality, non-standardised fermented products whose sensory richness arises from a variety of milk production and processing conditions. These practices would contribute to shaping microbial communities that have adapted to the dairy environment. In this most comprehensive study ever conducted on French PDO cheeses, our objective was to characterise the drivers of microbial communities in milks and the associated cheeses, and their relationships to biogeography, herd management and cheese processing practices. Thanks to the contribution of PDO cheese stakeholders, we sampled 1,145 PDO cheeses (each for rind and core) and 390 milks covering the diversity of the 44 French ripened PDO cheeses and collected detailed data on their production conditions. We characterised the bacterial and fungal communities of milks and cheeses using 16S rRNA and ITS2 gene sequencing. A total of 1,230 bacterial species and 1,367 fungal species were identified from the milk samples, with variations according to the dairy species. A total of 820 bacterial species and 333 fungal species were identified in cheeses. The core microbiome in cheese was limited to one fungal species (Geotrichum candidum) at 100% prevalence. The cheese’s microbiota differed in terms of richness and composition between the seven cheese families and within families, according to PDO labels. Secondary structuring factors, as the dairy species, the geographical area and cheese ripening practices, were also highlighted across cheese families, demonstrating a contribution of biogeography and PDO-specific know-how in shaping the cheese microbiota