EAGER: Transcriptome Assembly for a Molluscan Neurobiological Model

十多年来，被认为是有效的分子和遗传研究基础的首选工具是完全组装的基因组。加州海蜗牛具有简单的神经系统和较大的神经细胞，是研究行为神经基础的重要模型系统。埃里克·坎德尔博士在2000年被授予诺贝尔奖，主要是因为他在这个系统上的工作。2005年，一项由联邦政府资助的重大项目开始对这一重要模式物种的基因组进行测序和组装。由于大量的重复DNA序列和缺乏密切相关的基因组，基因组的完成既昂贵又具有挑战性。目前的项目将采用另一种方法：使用两个具有互补优势的下一代测序平台对RNA转录本（在大洋洲表达的基因）进行测序和组装。使用新开发的计算工具对这些applysia转录本进行测序、组装和注释将在巴尔的摩马里兰大学基因组科学研究所进行。这种“转录组优先”的方法关注的是在没有参考基因组的情况下转录组的组装，应该为其他研究团体在没有密切相关的参考基因组的情况下研究多样化的非脊椎动物物种提供一个重要的模型。数据将首先由一个顾问小组进行评估，该小组将由来自6至8个澳大利亚研究小组的代表组成。然后，数据将发布在applysia基因工具网站http://www.aplysiagenetools.org/上。该网站将提供初步RNA-seq组装，以及所有未来的初步和完整数据。此外，最终的注释转录组将提供给NCBI （www.ncbi.nlm.nih.gov）。通过已建立的软体动物神经科学门户（http://squishybrain.org/）的链接可以访问Aplysia基因工具网站，并且进展将通过MolluscNet的电子邮件列表进行沟通。数据传播的具体时间为：6个月：初步RNA-seq组装和初步注释，12个月：最终RNA-seq组装和更新注释，18个月：注释研讨会（涉及12-14个研究小组）后的最终注释，18个月，完成描述“转录组优先”策略和创新杂交RNA-seq组装的论文，~24个月：转录作图和靶向测序后的基因组注释。

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.