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

南极海鞘（Salpa thompsoni）是一种凝胶状浮游动物，是南大洋浮游生态系统的重要成员。实地研究证明，在有利的环境条件下，海鞘种群迅速增长，导致海鞘密集开花，大大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水平消耗，因此它的周期性优势有可能极大地改变生态系统的能量，并改变向深海的物质出口。 完成一个全面的参考基因组南极salp将能够识别基因和基因网络的生理反应，并允许检测潜在的过程驱动自然选择和物种？适应南极环境。 比较基因组分析将增加时间的维度，以推断生物体的适应性，并允许考虑其适应未来环境变化的潜力，并将允许检查只有在无脊椎动物类被囊动物中发现的基因组进化的新方面。完成的海鞘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研究这种被囊动物的快速基因组进化特征，并研究该物种的基因组基础？适应的潜力，特别是灵活的基因网络对成功应对不断变化的环境条件的作用。推动这项研究的主要假设是，预测S。Thompsoni直向同源物（即，具有相同功能的基因（具有共同祖先的基因）显示出快速进化的证据，这表明正选择，并且进一步地，这些基因和相关的基因网络为南极海鞘快速适应与变化的海洋相关的环境变化提供了基础。拟议的基因组组装策略将允许进一步的完善和脚手架的当前，高度碎片化的基因组组装使用的方法，在以前的工作。S. thompsoni现在存档在康州大学将进行分析，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。 高质量的参考组件将通过在单个个体上进行两次高输出配对末端测序运行（Illumina）以及在Oxford Nanopore长读测序仪上进行三次运行来获得。将对来自相同标本的组织的子采样进行相同的测序策略，以产生非常高质量的参考转录组，这将允许在基因组组装中进行高质量的基因模型和接近完整的基因预测。与尾索动物和头索动物物种的可用基因组数据的比较将增加分析的直系同源物的数量。Orthopathy基因将被测试的证据，快速选择的salp谱系，并将结果进行比较，以公布的表达谱和本体功能的salp。所有数据都将通过现有的门户网站公开提供;将开发一个项目网站，传播研究成果，供研究界和教育界查阅。网站设计将使用jbrowse的本地实例，它将提供注释，可下载的数据文件和以前发布的数据集的片段。

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.