Profiling transcriptome complexity and secondary metabolite synthesis in a benthic soft coral, Sinularia polydactyla

Transcriptome and metabolite responses to predation in a South pacific soft coral

Sinularia polydactyla, a dioecious, abundant soft coral in the South Pacific, exhibits biochemical phenotypic plasticity in secondary metabolite production in relation to predation intensity. However, it is unclear to what extent changes in secondary metabolites, such as 11beta-acetoxypukalide, may result from specific, induced pathway activities at the level of gene expression. To investigate both chemical changes and differences in mRNA diversity in response to predation stress, artificial predation experiments were conducted in situ on colonies of S. polydactyla. Multivariate statistical analyses of coral biochemical metabolites and our kinetic transcriptome profiling technique indicate that that the induction of 11beta-acetoxypukalide by predation stress likely results from the upregulation of either one dominant transcript or a very small set of transcripts, indicative of a targeted upregulation rather than a generalized, genetic stress response. Overall, this work establishes a routine method for integrating high-throughput transcriptome and metabolome data sets to allow for the identification of metabolites whose intracellular concentrations can be readily linked to gene expression events in response to specific treatments in non-model organisms.

A functional approach to transcriptome profiling: linking gene expression patterns to metabolites that matter

Secondary metabolites or natural products have been isolated from many marine organisms. These metabolites often have important bioactive functions; however, very little information is available regarding the biosynthesis and regulation of many secondary metabolites. At a time when use of marine-derived metabolites is rapidly expanding in industry and pharmacological fields, a better understanding of the genetic mechanisms controlling secondary metabolite production is necessary. We review the recent development of a novel transcriptome profiling methodology that allows for rapid and high-throughput screening of changes in mRNA sequence pools. The application of genomics-based techniques and the integration of both biochemical and molecular data sets in marine organisms complement ongoing drug discovery efforts.

Gene expression profiling of two related soft corals, Sinularia polydactyla and S. maxima, and their putative hybrid at different life-history stages

The soft coral species, Sinularia polydactyla and Sinularia maxima are abundant in shallow coral reef habitats in Guam. Both species are gonochoric and mass spawning events can result in an apparent S. polydactyla-S. maxima hybrid exhibiting morphological characteristics of both parents. These morphological differences prompted our investigation of potential differences in gene expression patterns among these closely related species. In concert with interspecific level differences, intraspecific level differences in transcriptome diversity and complexity were also studied among juvenile, adult male, and adult female S. polydactyla colonies. To uncover these transcriptome-level differences, RNA was extracted from RNAlater(R)-preserved samples and cDNA libraries constructed using a nano-scale synthesis strategy. Changes in transcriptome complexity (mRNA sequence composition) of these libraries were measured using reannealing rate assays that employ an informatics-based analysis of kinetic profiles. This method allows for quick, high-throughput analysis of sequence complexity and has been used to compare transcriptome-level differences in other marine invertebrates. Comparisons of transcriptome data revealed diagnostic differences in the transcriptome pools. Examination of transcriptome changes in closely related species experiencing similar environmental parameters may enable us to understand developmental, morphological, and sex-specific changes in gene expression patterns.