SGER: Life at Depth: A Comparative Genomics Perspective

这笔赠款利用相当大的现有支持，对四种深海微生物的基因组进行关闭、完成、注释和进行比较基因组学分析。由于戈登和贝蒂·摩尔基金会的海洋微生物学倡议，所有这些生物都已经或正在进行测序。目标是开发一个基因组序列平台，由所有已知的五个嗜压(高压适应)细菌属组成，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模体。被检测的微生物有：1)深层发光菌3TCK，2)本氏希万氏菌KT99，3)冷单胞菌。菌株CNPT3和4)Moritella sp.菌株PE36。3TCK与深水假单胞菌SS9同属一种压敏性菌株。KT99是生长最快的极端嗜压生物，也是最常见的孤立嗜压物种的一员。CNPT3和PE36是研究得最好的两种压电剂。现有的DNA序列将被重组，序列覆盖率较低的区域将被重新测序。差距将通过末端测序、BAC和Fosid文库以及加入聚合酶链式反应来弥合。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，并由鹊类基因组注释系统管理。最终，基因组将与比较的压电性和相关的压敏菌株的基因组一起被合并到MySQL关系数据库中。将确定菌株之间的插入/缺失和基因组重排，并探索蛋白质基序、氨基酸替换、密码子使用以及tRNA和rRNA结构的可能差异。将确定深海变异的正选择基因，并将对选定的与压力者相关的推导出的感兴趣基因产物的三维结构进行建模。这些努力的结果将是对生物圈最大部分--深海--生命蓝图的前所未有的看法。这位研究人员正在组织一份杂志和视频，描述斯克里普斯研究所的海洋基因组学活动。面向公众的海洋学。

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.