SGER: Life at Depth: A Comparative Genomics Perspective

这项资助利用了相当多的现有支持，对四种深海微生物的基因组进行关闭、完成、注释和比较基因组分析。所有这些生物都已经或正在进行测序，这是戈登和贝蒂·摩尔基金会海洋微生物学倡议的结果。目标是开发一个基因组序列平台，包括所有五个已知的嗜压（高压适应）细菌属，并利用这一资源定位与海洋深处生命相关的基因和蛋白质基序。检出的微生物有：1)深光杆菌3TCK， 2)希瓦氏菌KT99, 3)冷单胞菌CNPT3和4)森利菌PE36。3TCK是一种压力敏感的成员，与嗜压性P. profundum菌株SS9属于同一物种。KT99是生长最快的极端嗜压菌，也是最常见的分离嗜压菌。CNPT3和PE36是研究得最好的两种亲压试剂。可用的DNA序列将被重新组装，序列覆盖率差的区域将被重新测序。缺口将通过末端测序BAC和fosmid文库以及加入聚合酶链反应来关闭。由此产生的封闭基因组将使用各种软件工具和算法进行注释，以分析基因组和蛋白质序列数据，并由MAGPIE基因组注释系统进行管理。最终，基因组将与比较嗜压菌株和相关压敏感菌株的基因组一起纳入MySQL关系数据库。将鉴定菌株之间的插入/缺失和基因组重排，并探索蛋白质基序、氨基酸取代、密码子使用以及tRNA和rRNA结构可能存在的差异。在深海正选择变异下的基因将被识别，选定的与嗜压菌相关的推断基因产物的三维结构将被建模。这些努力的结果将是前所未有地看到生物圈最大部分的生命蓝图：深海。研究人员正在为公众组织一本杂志和视频，介绍斯克里普斯海洋学研究所的海洋基因组学活动。

This grant leverages considerable existing support to close, finish, annotate and perform comparative genomics analyses on the genomes of four deep-sea microbes. All of these organisms have been or are being sequenced as a result of the Gordon and Betty Moore Foundation Marine Microbiology Initiative. The goal is to develop a genome sequence platform, consisting of all five known genera of piezophilic (high pressure-adapted) bacteria, and to use this resource to locate genes and protein motifs that correlate with life in the depths of the oceans. The organisms to be examined are 1) Photobacterium profundum strain 3TCK, 2) Shewanella benthica strain KT99, 3) Psychromonas sp. strain CNPT3 and 4) Moritella sp. strain PE36. 3TCK is a pressure-sensitive member of the sames species as the piezophile P. profundum strain SS9. KT99 is the fastest growing extreme piezophile and is a member of the most commonly isolated piezophilic species. CNPT3 and PE36 are two of the best studied piezophiles. The available DNA sequences will be reassembled and areas of poor sequence coverage will be resequenced. Gaps will be closed by end sequencing BAC and fosmid libraries and by joining polymerase chain reactions. The resulting closed genomes will be annotated using a variety of software tools and algorithms to analyze genome and protein sequence data and managed by the MAGPIE genome annotation system. Eventually the genomes will be incorporated into a MySQL relational database along with the genomes of comparison piezophilic and related piezosensitive strains. Insertions/deletions and genome rearrangements among strains will be identified and possible differences in protein motifis, amino acid substitutions, codon usage and tRNA and rRNA structure will be explored. Genes under positive selection for variation in the deep sea will be identified, and the three-dimensional structure of selected piezophile-relevant deduced gene products of interest will be modeled. The result of these efforts will be an unprecedented view of the blue prints of life in the largest part of the biosphere: the deep ocean. The investigator is organizing a magazine and video description of marine genomics activities at Scripps Inst. Oceanography for the public.