| 项目编号: | 1643825
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| 项目名称: | Genome Assembly and Analysis of the Bloom Forming Southern Ocean Salp, Salpa Thompsoni |
| 作者: | Ann Bucklin
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| 承担单位: | University of Connecticut
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| 批准年: | 2017
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| 开始日期: | 2017-09-15
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| 结束日期: | 2020-08-31
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| 资助金额: | 250039
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| 资助来源: | US-NSF
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| 项目类别: | Standard Grant
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| 国家: | US
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| 语种: | 英语
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| 特色学科分类: | Geosciences - Polar
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| 英文关键词: | antarctic salp
; salp
; genome assembly strategy
; dense bloom
; gene
; gene network
; deep ocean
; fragmented genome assembly
; genome assembly
; salp lineage
; high-quality reference assembly
; species
; southern ocean pelagic ecosystem
; salp reference genome
; comprehensive reference genome
; comparative genomic analysis
; rapid genome evolution characteristic
; salp genome assembly
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| 英文摘要: | 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. |
| 资源类型: | 项目
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| 标识符: | http://119.78.100.158/handle/2HF3EXSE/88774
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| Appears in Collections: | 全球变化的国际研究计划
科学计划与规划
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| Recommended Citation: | |
Ann Bucklin. Genome Assembly and Analysis of the Bloom Forming Southern Ocean Salp, Salpa Thompsoni. 2017-01-01.
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