Project description:Both single cell and bulk RNA sequencing was performed on expanding or differentiating snake venom gland organoids (from Aspidelaps Lubricus Cowlesi and Naja Nivea), or tissue (Aspidelaps Lubricus Cowlesi). Bulk RNA sequencing from the snake venom gland, liver and pancreas was performed to construct a de novo transcriptome using Trinity.
Project description:Transcriptome sequencing of non-model organisms is valuable resource of the genetic basis of ecological-meaningful traits. The Royal Irises, Iris section Oncocyclus (Iris: Iridaceae, order Asparagales), are a Middle-East group of species in the course of speciation. The species are characterized with extremely large flowers, a huge range of flower colors and a unique pollination system. The Royal Irises, which are a symbol of conservation in the Middle-east, serve as a model for evolutionary processes of speciation and plant ecology. However, there are not sufficient transcriptomic and genomic data for molecular characterization. Thus, it is necessary to generate massive transcript sequences for functional characterization and molecular marker development for the Royal Irises. The Iris transcriptome sequencing provides valuable resource for studying adaptation-associated traits in this non-model plant. Although intensive eco-evolutionary studies, this is the first reported transcriptome for the Royal Irises. The data available from this study will facilitate gene discovery, functional genomic studies and development of molecular markers in irises, and will provide genetic tools for their conservation.
Project description:While the vertebrate body plan is highly conserved amongst all species of this taxon, extreme variations thereof can be documented in snakes, which display both an absence of limbs and an unusually elongated trunk. As Hox genes are strong candidates both for the making and the evolution of this body plan, their comparative study in such a morphologically diverged group is informative regarding their potential causative importance in these processes. In this work we use an interspecies comparative approach where different aspects of regulation at the HoxD locus are investigated. We find that although spatial collinearity and associated epigenetic mark dynamics are conserved in the corn snake, other regulatory modalities have been largely restructured. A BAC transgenic approach indeed revealed that, while the majority of mesodermal enhancers in vertebrates appear to be mostly located outside of the cluster, the corn snake contains most mesodermal trunk enhancers within the HoxD cluster. We also find that, despite the absence of limbs and an altered Hoxd gene regulation in external genitalia, the bimodal chromatin structure at the corn snake HoxD locus is maintained. The analysis of particular enhancer sequences initially defined in the mouse and further isolated at the snake orthologous locus showed differences in their specificities for the limb and genital bud expression. Of particular interest, a snake counterpart of a mouse limb-only enhancer sequence evolved into a genital-only enhancer. Such a regulatory exaptation suggests that enhancer versatility may have been an important factor to accompany the transition towards the snake body plan. These results show that vertebrate morphological evolution is likely to have been associated with extensive reorganization at the HoxD regulatory landscapes while respecting a very conserved general regulatory framework.