Genome Assembly and Analysis of the Bloom Forming Southern Ocean Salp, Salpa Thompsoni

南大洋樽海鞘藻华的基因组组装和分析，Salpa Thompsoni

• 批准号: 1643825
• 负责人: Ann Bucklin
• 金额: $ 25万
• 依托单位: University of Connecticut
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2021-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1643825&HistoricalAwards=false
• 关键词: Genome; Assembly; Analysis; Bloom; Forming

The Antarctic salp, Salpa thompsoni, is a gelatinous zooplankton that is an important member in the Southern Ocean pelagic ecosystem. Field studies have documented rapid population growth under favorable environmental conditions, resulting in dense blooms of salps that substantially change the pelagic ecosystem in regards to both structure and processes. Because this zooplankton can proliferate rapidly and it is not readily consumed by upper trophic levels, its periodic dominance has the potential to drastically chance ecosystem energetics as well as change material export to the deep ocean. Completion of a comprehensive reference genome for the Antarctic salp will enable the identification of genes and gene networks underlying physiological responses and allow detection of potential processes driving natural selection and the species? adaptation strategies to the Antarctic Environment. Comparative genomic analysis will add the dimension of time to inferences about organismal adaptation and allow consideration of their potential to adapt to future environmental changes, and will allow examination of novel aspects of genomic evolution found only in the invertebrate class Tunicata. The completed salp reference genome will provide a valuable foundational resource for other scientists working on this species as well as the genomic basis for function and adaptation in the Antarctic. The primary goal of this effort is to examine the rapid genome evolution characteristic of this tunicate species and examine the genomic bases of the species? potential for adaptation, and specifically the role of flexible gene networks for successful responses to changing environmental conditions. The primary hypothesis driving this research is that predicted S. thompsoni orthologs (i.e., genes of the same function that share a common ancestor) that show evidence of rapid evolution are indicative of positive selection, and further that these genes and associated gene networks provide the basis for rapid adaptation of the Antarctic salp to environmental variation associated with a changing ocean. The proposed genome assembly strategy will allow further refinements and scaffolding of the current, highly fragmented genome assembly using the methods developed during previous work. Specimens of S. thompsoni now archived at UConn will be analyzed to improve the salp genome assembly, increasing overall scaffold length, and decreasing the number of total contigs. High-quality reference assemblies will be obtained with two high-output paired-end sequencing runs (Illumina) on a single individual, coupled with three runs on the Oxford Nanopore long-read sequencer. The same sequencing strategy will be performed on a sub-sampling of tissues from the same specimen to produce a very high quality reference transcriptome, which will allow for high quality gene models and near-complete gene predictions in the genome assembly. Comparisons with available genomic data for Urochordate and Cephalochordate species will increase the number of orthologs analyzed. Orthologous genes will be tested for evidence of rapid selection in the salp lineage, and the results will be compared to published expression profiles and ontology functions for the salp. All data will be made publicly available via existing web portals; a project website will be developed to disseminate research results for access by the both research and educational communities. Website design will use a local instance of jbrowse that will offer annotations, downloadable data files, and tracts of previously-published datasets.

南极盐藻Salpa thompsoni是一种胶状浮游动物，是南大洋远洋生态系统中的重要成员。实地研究证明，在有利的环境条件下，种群迅速增长，导致盐碱地密集繁殖，极大地改变了远洋生态系统的结构和过程。由于这种浮游动物可以迅速繁殖，而且不容易被上层营养层消耗，它的周期性优势有可能极大地影响生态系统能量学，并改变向深海的物质出口。完成南极Salp的全面参考基因组将能够识别潜在的生理反应的基因和基因网络，并能够检测驱动自然选择和物种？适应南极环境的战略。比较基因组分析将增加关于有机体适应的推断的时间维度，并允许考虑它们适应未来环境变化的潜力，并将允许检查仅在无脊椎动物纲中发现的基因组进化的新方面。完成的SALP参考基因组将为研究该物种的其他科学家提供宝贵的基础资源，并为南极的功能和适应提供基因组基础。这项工作的主要目标是检查这种被囊状物种的快速基因组进化特征，并检查该物种的基因组基础？适应的潜力，特别是灵活的基因网络在成功应对不断变化的环境条件方面的作用。推动这项研究的主要假设是，预测的汤普森链霉菌同源基因(即具有相同功能的基因，共享共同的祖先)表明快速进化的证据表明了正向选择，而且这些基因和相关的基因网络为南极盐碱地快速适应与海洋变化相关的环境变化提供了基础。拟议的基因组组装战略将允许使用之前工作中开发的方法对当前高度分散的基因组组装进行进一步完善和搭建。目前在康涅狄格州大学存档的桑普森葡萄球菌样本将被分析，以改善SALP基因组组装，增加总支架长度，并减少总重叠群的数量。通过在单个个体上进行两次高输出的成对末端测序(Illumina)，以及在牛津纳米孔长读测序仪上进行三次测序，将获得高质量的参考组件。同样的测序策略将在同一样本的组织的子样本上进行，以产生非常高质量的参考转录组，这将允许在基因组组合中进行高质量的基因模型和接近完整的基因预测。与现有的尿索类和头索类物种的基因组数据进行比较，将增加分析的同源基因的数量。将对SALP谱系中的同源基因进行快速选择的证据进行测试，并将结果与已公布的SALP表达谱和本体功能进行比较。所有数据将通过现有的门户网站向公众开放；将开发一个项目网站，以传播研究成果，供研究和教育界查阅。网站设计将使用JBrowse的本地实例，该实例将提供注释、可下载的数据文件和以前发布的数据集的区域。