SeaBase: A Multispecies Transcriptomic Resource and Platform for Gene Network Inference

Abstract

Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide-ranging capabilities. Genomics tools are essential for taking advantage of these "free lessons" of nature. However, genomics and transcriptomics are challenging in emerging model systems. Here, we present SeaBase, a tool for helping to meet these needs. Specifically, SeaBase provides a platform for sharing and searching transcriptome data. More importantly, SeaBase will support a growing number of tools for inferring gene network mechanisms. The first dataset available on SeaBase is a developmental transcriptomic profile of the sea anemone Nematostella vectensis (Anthozoa, Cnidaria). Additional datasets are currently being prepared and we are aiming to expand SeaBase to include user-supplied data for any number of marine and aquatic organisms, thereby supporting many potentially new models for gene network studies. SeaBase can be accessed online at: http://seabase.core.cli.mbl.edu.

NvERTx: a gene expression database to compare embryogenesis and regeneration in the sea anemone Nematostella vectensis

“…Since then, a large number of developmental genes have been identified in Nematostella, and many commonalities between Nematostella and bilatarian development have emerged (Amiel et al, 2017;Burton and Finnerty, 2009;Darling et al, 2005;Genikhovich et al, 2015;Layden and Martindale, 2014;Layden et al, 2012;Leclere et al, 2016;Matus et al, 2008;Meyer et al, 2011;Reitzel et al, 2007;Röttinger et al, 2012). With the advent of high-throughput transcriptomics, several studies have examined gene expression during embryogenesis at the whole-genome level (Helm et al, 2013;Fischer and Smith, 2013;Fischer et al, 2014;Tulin et al, 2013), firmly establishing Nematostella as an embryonic model. More recently, Nematostella has shown to be a powerful model for regeneration.…”

“…To facilitate this line of study, we created N.vectensis Embryogenesis and Regeneration Transcriptomics (NvERTx)a quantitative gene expression database for comparing embryogenesis and regeneration in the sea anemone N. vectensis. NvERTx comprises several data sets spanning embryogenesis (Helm et al, 2013;Fischer and Smith, 2013;Fischer et al, 2014;Tulin et al, 2013; this study) and regeneration (this study). We used pooled RNA sequencing (RNAseq) data from Nematostella embryogenesis and regeneration to generate a de novo transcriptome assembly.…”

Recent advances in genomics and transcriptomics of cnidarians

“…These include transcriptomes of Nematostella at different developmental stages Helm et al, 2013;Fredman et al, 2013), but also of Edwardsiella lineata, a species closely related to Nematostella (Stefanik et al, 2014) and corals (Karako-Lampert et al, 2014;Pooyaei Mehr et al, 2013). These data are publicly available and some of them are stored in a database (Fischer et al, 2014), which will certainly support further research activities in cnidarian development and evolution.…”

Addressing Grand Challenges In Organismal Biology: The Need For Synthesis

“…We need to identify transdisciplinary principles, approaches, and frameworks that are robust to their context. Examples include the general properties of networks (e.g., Cowan et al 2012, Fischer et al 2014, Nijhout and Reed 2014, which can be applied to gene networks, neural networks, and interaction networks and even to social networks. For the development of predictive models and methods necessary to identify general patterns and overarching principles, we need to define and articulate the limits of biological questions such that appropriate modeling techniques can be applied.…”