SGER: Life at Depth: A Comparative Genomics Perspective

这笔赠款利用现有的大量支持，对四种深海微生物的基因组进行关闭，完成，注释和比较基因组学分析。由于戈登和贝蒂摩尔基金会海洋微生物学倡议，所有这些生物都已经或正在测序。 目标是开发一个基因组序列平台，包括所有五种已知的嗜压（高压适应）细菌，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。待检微生物为：1）深水发光杆菌菌株3 TCK，2）海底希瓦氏菌菌株KT 99，3）冷单胞菌菌株CNPT 3和4）森氏菌菌株PE 36。 3 TCK是与P. profundum菌株SS 9相同种的压力敏感成员。 KT 99是生长最快的极端嗜压菌，也是最常见的嗜压菌种。 CNPT 3和PE 36是两种研究得最好的亲压体。 将重组可用的DNA序列，并对序列覆盖率低的区域进行重新测序。 将通过末端测序BAC和fosmid文库以及通过连接聚合酶链反应来闭合缺口。 将使用各种软件工具和算法对所得到的封闭基因组进行注释，以分析基因组和蛋白质序列数据，并由MAGPIE基因组注释系统管理。 最终，基因组将与比较嗜压菌株和相关的压电敏感菌株的基因组一起沿着纳入MySQL关系数据库。 将确定菌株之间的插入/缺失和基因组重排，并探讨蛋白质基序、氨基酸取代、密码子使用以及tRNA和rRNA结构的可能差异。 将确定在深海中正选择变异的基因，并将模拟选定的与嗜压体有关的感兴趣的推断基因产物的三维结构。 这些努力的结果将是对生物圈最大部分的生命蓝图的前所未有的看法：深海。该研究员正在为公众组织一份关于斯克里普斯海洋研究所海洋基因组学活动的杂志和视频说明。

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.