Project description:Venoms have convergently evolved in all major animal lineages and are ideal candidates to unravel the underlying genomic processes of convergent trait evolution. However, few animal groups have been studied in detail, and large-scale comparative genomic analyses to address toxin gene evolution are rare. Hyper-diverse hymenopterans are the most speciose group of venomous animals, but the origin of their toxin genes have been largely overlooked. We combined proteo-transcriptomics with comparative genomics compiling an up-to-date list of core bee venom proteins to investigate the origin of 11 venom genes in 30 hymenopteran genomes including two new stingless bees.
Project description:Venoms have convergently evolved in all major animal lineages and are ideal candidates to unravel the underlying genomic processes of convergent trait evolution. However, few animal groups have been studied in detail, and large-scale comparative genomic analyses to address toxin gene evolution are rare. Hyper-diverse hymenopterans are the most speciose group of venomous animals, but the origin of their toxin genes have been largely overlooked. We combined proteo-transcriptomics with comparative genomics compiling an up-to-date list of core bee venom proteins to investigate the origin of 11 venom genes in 30 hymenopteran genomes including two new stingless bees.
Project description:Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the concept of tacking trait enabling natural selection of fitness-costly metabolic traits. The concept is inspired from the tacking maneuver used in sailing for traversing upwind. We use first-principle metabolic models to design an evolution niche wherein the tacking trait and fitness become correlated. Adaptive evolution in this niche, when followed by the reversal to the original niche, manifests in the improvement of the desired trait due to biochemical coupling between the tacking and the desired trait. We experimentally demonstrate this strategy, termed EvolveX, by evolving wine yeasts for increased aroma production. Our results pave the way for precision laboratory evolution for biotechnological and ecological applications.
Project description:To assess plasticity in genetic regulation of gene expression in Arabidopsis thaliana, genome wide gene expression variation was analyzed in a Ler/Cvi recombinant inbred line (RIL) population treated with low-light. The variation in expression could be explained for many genes by expression quantitative trait loci (eQTLs), which were compared to a previous genetical genomics study in the same untreated population. Please note Characteristics[StrainOrLine] is the population of 162 recombinant inbred lines between the accessions Ler x Cvi. Ler and Cvi are the names of the parental accessions.
Project description:Adaptive laboratory evolution is highly effective for improving desired traits through natural selection. However, its applicability is inherently constrained to growth-correlated traits precluding traits of interest that incur a fitness cost, such as metabolite secretion. Here, we introduce the concept of tacking trait enabling natural selection of fitness-costly metabolic traits. The concept is inspired from the tacking maneuver used in sailing for traversing upwind. We use first-principle metabolic models to design an evolution niche wherein the tacking trait and fitness become correlated. Adaptive evolution in this niche, when followed by the reversal to the original niche, manifests in the improvement of the desired trait due to biochemical coupling between the tacking and the desired trait. We experimentally demonstrated this strategy, termed EvolveX, by evolving wine yeasts for increased aroma production. RNA-sequencing was performed for parental and evolved strains in the respective evolution niche and in natural grape must.
Project description:Inferring the heritability of gene expression is one of the main areas of the field of genetical genomics. With the possibility to treat the abundances of gene transcripts as a suite of quantitative traits, genetical genomics can make an extensive use of the microarray technology. Here we extended a major method for estimating the heritability of a quantitative trait, single parent-offspring regression, to assess the heritability of the expression of genes with two-channel microarrays. In a series of maternal parent-offspring pairs of Interior spruce (Picea glauca x engelmannii, our focus in the outer stem tissues is the expression of defense-related genes, the heritability of which can affect fitness and necessary for evolution by natural selection.
Project description:Expression quantitative trait locus (QTL) mapping of 127 adult femoral bone samples from a Red Junglefowl x White Leghorn advanced intercross line. Bone trait QTL have been mapped in the same cross, allowing a genetical genomics approach to quantitative trait gene identification
Project description:As Asians are underrepresented across many omics databases limiting the potential of precision medicine of the global population. It is thus important for multi-omics derived quantitative trait loci (QTLs) to fill the knowledge gap of complex traits in the Asian ancestry. Integrating omics data from genomics and epigenomics (including DNA methylation and RNA-seq from blood), we developed iMOMdb, an open-acesss database to enhance disease prediction models and precision medicine outcomes in Asian pregnant women.