Transcriptional Responses of Resistant and Susceptible Fish Clones to the Bacterial Pathogen Flavobacterium psychrophilum

Flavobacterium psychrophilum is a bacterial species that represents one of the most important pathogens for aquaculture worldwide, especially for salmonids. To gain insights into the genetic basis of the natural resistance to F. psychrophilum, we selected homozygous clones of rainbow trout with contrasted susceptibility to the infection. We compared the transcriptional response to the bacteria in the pronephros of a susceptible and a resistant line by micro-array analysis five days after infection. While the basal transcriptome of healthy fish was significantly different in the resistant and susceptible lines, the transcriptome modifications induced by the bacteria involved essentially the same genes and pathways. The response to F. psychrophilum involved antimicrobial peptides, complement, and a number of enzymes and chemokines. The matrix metalloproteases mmp9 and mmp13 were among the most highly induced genes in both genetic backgrounds. Key genes of both pro- and anti-inflammatory response such as IL1 and IL10, were up-regulated with a greater magnitude in susceptible animals where the bacterial load was also much higher. While higher resistance to F. psychrophilum does not seem to be based on extensive differences in the orientation of the immune response, several genes including complement C3 showed stronger induction in the resistant fish. They may be important for the variation of susceptibility to the infection

Analysis of expressed sequence tags from Actinidia : Applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

Background Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs). Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia

Variation of interspecific interactions at different ecological levels within an assemblage of Arctic marine predators

International audienceHow interspecific interactions change across scales is poorly known. Such knowledge might help us understand how species interact within communities and highlight scale-dependent ecological processes in play among species. Here, I propose to analyze the inter-annual variation of a species assemblage at different ecological levels. For this, I joined a two-stage modeling approach and a spatially explicit multivariate model to analyze the interspecies relationships among six species of pelagic seabirds from 2004 to 2015 in the Barents Sea. The large-scale (~400 km) pattern of interactions revealed by the analyses suggests a change in the composition of the seabird community along the climatic gradient from south to north. At medium-scale (~300 km), the community was split into two areas (i.e., Arctic and sub-Arctic areas) suggesting niche differentiation of Arctic and sub-Arctic species driven by resource partitioning and interference competition. At a small-scale (~40 km), species with different body sizes were positively associated suggesting facilitation for accessing food although the species with the smallest body size was negatively associated with the species involved in the facilitation process suggesting interspecific interference competition. Over the years, the large-scale patterns were persistent, suggesting niche establishment, while small-scale patterns were highly variable suggesting only ephemeral interactions among species. My study demonstrates that interspecific relationships are scale-dependent and play major roles in structuring community. Untangling how species are associated with different ecological levels over time is indispensable to better understand how community structure contributes to ecological system dynamics