EAGER: Transcriptome Assembly for a Molluscan Neurobiological Model

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For over a decade, the preferred tool that has been considered to be the basis for effective molecular and genetic studies has been a fully assembled genome. Because of its simple nervous system and large nerve cells, the marine snail Aplysia californica is an important modelsystem for studies of the neural basis of behavior. Dr. Eric Kandel was awarded the Nobel Prize in 2000 primarily for his work on this system. In 2005, a major federally-funded effort was begun to sequence and assemble the genome of this important model species. Because of large amounts of repeat DNA sequences in Aplysia and the lack of a closely related genome, the completion of the genome has been both costly and challenging. The present project will take an alternative approach: sequencing and assembly of RNA transcripts (the genes expressed in Aplysia) using two Next Generation sequencing platforms that have complementary advantages. The sequencing, assembly and annotation of these Aplysia transcripts using newly developed computational tools will be conducted at the Institute for Genome Sciences at the University of Maryland, Baltimore. This focus on the transcriptome assembly in the absence of a reference genome, a "transcriptome-first" approach, should provide an important model for other research communities working on diverse, non-vertebrate species without a closely related reference genome. Data will first be evaluated by an advisory panel, which will comprise representatives from between six and eight Aplysia research groups. Data will then be posted on an Aplysia Gene Tools website, http://www.aplysiagenetools.org/. This site will host the preliminary RNA-seq assembly as it becomes available, as well as all future preliminary and complete data. Additionally a finalized annotated transcriptome will be provided to NCBI (ww.ncbi.nlm.nih.gov). The Aplysia Gene Tools web site will be accessible via links from the established Molluscan Neuroscience Gateway (http://squishybrain.org/), and progress will be communicated with the MolluscNet email list. The specific timelime for data dissemination is as follows: 6 months: preliminary RNA-seq assembly and preliminary annotation, 12 months: final RNA-seq assembly and updated annotation, 18 months: final annotation following annotation workshop (involving 12-14 research groups), 18 months, completion of paper describing "transcriptome-first" strategy and innovative hybrid RNA-seq assembly, ~24 months: annotation of genome following transcript mapping and targeted sequencing.