Transcriptome resources for a cephalopod model system

头足类动物模型系统的转录组资源

• 批准号: 8512338
• 负责人: Clifton W. Ragsdale
• 金额: $ 7.62万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-04-01 至 2015-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8512338
• 关键词: Amputation; Animal Model; Animals; Archives; Award; Bioinformatics; Biological Models; Biology; Brain; California; Chicago; Collaborations; Communities; Complementary DNA; Data; Data Analyses; Data Set; Databases; Deposition; Development; Embryo; Embryology; Embryonic Development; Engineering; Funding; Gene Delivery; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Generations; Genes; Genome; Genomics; Goals; Haploidy; Human; Human Genome; Immunohistochemistry; In Situ Hybridization; Informatics; Institutes; Invertebrates; Investigation; Laboratories; Methods; Modeling; Molecular; Names; Natural regeneration; Nerve Regeneration; Neuraxis; Octopus; Organism; Pattern; Plasmids; Preparation; Publications; Rattus; Regenerative Medicine; Regulator Genes; Repetitive Sequence; Research; Research Project Grants; Resources; Science; Short Tandem Repeat; Site; Spottings; Squid; Staging; Structure; Technology; Tissues; Transcript; Universities; Vertebrates; Work; arm; cDNA Library; comparative; deep sequencing; egg; expression vector; gene discovery; genome annotation; genome sequencing; meetings; neurodevelopment; novel; programs; public health relevance; transcriptomics; web site

DESCRIPTION (provided by applicant): The long-term goal of this project is a cephalopod model system for studies into mechanisms of embryogenesis, neural development and regeneration. Among animals, human beings are large organisms with disproportionately large brains. Cephalopods, which include squids and octopuses, are the largest non-mammalian organisms and have the largest brains among all invertebrates. They also have a cellular pattern of early embryogenesis that is strikingly similar to that of vertebrates. To study cephalopod development at a mechanistic level requires the identification of a cephalopod species with ready availability, easy husbandry and an embryology permitting experimental manipulation. We have identified such a preparation, the California Two-spot Octopus (O. bimaculoides). An important additional advantage in choosing an octopus for a cephalopod model system is that octopus arms, each of which contains a massive central nervous system, regenerate rapidly after amputation and could serve as a new model in regenerative medicine. To date, we have developed methods for octopus in situ hybridization and immunohistochemistry, engineered an octopus plasmid expression vector and demonstrated gene delivery into octopus embryos and arm tissue. We have also isolated cDNAs for a small panel of octopus developmental regulatory genes by degenerate primer PCR and through plasmid cDNA library sequencing. For O. bimaculoides to be a credible model system will, however, require a much greater depth of information about octopus gene expression and regulation. The first aim of the proposed work is to develop RNAseq databases for O. bimaculoides using state-of-the-art sequencing technologies and assembly programs. The second aim is to apply this transcriptome information about message structure to a concurrent O. bimaculoides genome sequencing project, and to build out a cephalopod community web site (www.cephseq.org) for sharing sequence data. Cephalopod genomes are large and repeat-rich so transcriptome data will be essential for genome assembly and annotation. The generation of these transcriptomic and genomic resources will drive hypothesis-driven research on the molecular and cellular mechanisms of cephalopod development and regeneration.

描述（由申请人提供）：本项目的长期目标是研究胚胎发生、神经发育和再生机制的头足类动物模型系统。在动物中，人类是具有不成比例的大脑的大型生物。包括鱿鱼和章鱼在内的鲸类是最大的非哺乳类生物，在所有无脊椎动物中拥有最大的大脑。它们也有一个早期胚胎发生的细胞模式，与脊椎动物惊人地相似。研究头足类动物的发展机制的水平，需要确定一个头足类物种容易获得，易于饲养和胚胎学允许实验操作。我们已经确定了这样一种制剂，加州双点章鱼（O。bimaculoides）。选择章鱼作为头足类动物模型系统的另一个重要优势是，章鱼的手臂，每个手臂都包含一个巨大的中枢神经系统，在截肢后迅速再生，可以作为再生医学的新模型。到目前为止，我们已经开发了章鱼原位杂交和免疫组织化学的方法，设计了章鱼质粒表达载体，并证明了基因传递到章鱼胚胎和手臂组织。我们还通过简并引物PCR和质粒cDNA文库测序分离了一小组章鱼发育调控基因的cDNA。O.然而，bimaculoides要成为一个可信的模型系统，需要更深入的关于章鱼基因表达和调控的信息。本研究的第一个目标是建立O. bimaculoides使用国家的最先进的测序技术和组装程序。第二个目标是将这些关于消息结构的转录组信息应用于并发O。bimaculoides基因组测序计划，并建立了一个头足类动物社区网站（www.cephseq.org），用于共享序列数据。鲸足类基因组大且重复序列丰富，因此转录组数据对于基因组组装和注释至关重要。这些转录组和基因组资源的产生将推动头足类动物发育和再生的分子和细胞机制的假设驱动的研究。