Microbial Genome Sequencing: Complete Genome Sequences of Green Bacteria

微生物基因组测序：绿色细菌的完整基因组序列

• 批准号: 0523100
• 负责人: Donald Bryant
• 金额: --
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0523100&HistoricalAwards=false
• 关键词: Microbial; Genome; Sequencing; Complete; Sequences

Photosynthetic bacteria convert light into chemical energy for the subsequent fixation of carbon dioxide from the atmosphere into biomass. These organisms account for 50% of all photosynthesis, and thus they insure the continued existence of life on Earth. In this study, the genome sequences of 15 photosynthetic bacteria will be completed, annotated and compared. Green Sulfur Bacteria (GSB) are major primary producers in anoxic environments, where they contribute significantly to the biogeochemical cycling of carbon, nitrogen, and sulfur on Earth. Until recently, genome information was only available for Chlorobium tepidum, a possibly atypical organism from a sulfide-rich hot spring. The Joint Genome Institute (JGI-DOE) has completed draft sequences for eight GSB, and a ninth GSB genome will be sequenced in 2005. JGI-DOE will also produce high-quality draft sequences for seven members of the Chloroflexi, six of which are Filamentous Anoxygenic Phototrophs (FAPs; formerly, green gliding/non-sulfur bacteria). Only an incomplete draft sequence for one FAP, Chloroflexus aurantiacus is currently available. Recent studies suggest that FAPs are physiologically diverse and widely distributed in nature. Newly described isolates can fix carbon using different pathways, fix nitrogen, and oxidize sulfide and possibly ferrous iron and other metals. FAPs are important but poorly characterized components of terrestrial, freshwater and saline environments, and whole-genome analyses will provide many new insights into their properties. Many scientists are currently studying photoautotrophic metabolism, the mechanisms and origins of photosynthesis, and the evolutionary relationships among photoautotrophs. These issues will be directly addressed in this study through whole-genome sequencing and subsequent comparative bioinformatic analyses of the data. Since it will be the largest and most comprehensive database ever assembled for both GSB and FAPs, the data obtained in this study will have very broad impact. The finished sequences will be deposited in public databases, and these data, as well as the automatic and manual annotation data, will also be made available via a publicly accessible website. Two postdoctoral scientists and four undergraduate researchers will be trained during the execution of this research program. The PI and Co-PI will organize a course for advanced undergraduates and graduate students that will provide both passive and active learning experiences in Microbial Genomics and Bioinformatics. This course will fill an existing void in the microbiology and bioinformatics curriculum at The Pennsylvania State University.

光合细菌将光转化为化学能，随后将大气中的二氧化碳固定为生物质。这些生物占所有光合作用的50%，因此它们确保了地球上生命的持续存在。本研究将完成15种光合细菌的基因组序列，并进行注释和比较。绿色硫细菌（GSB）是缺氧环境中的主要初级生产者，在那里它们对地球上碳、氮和硫的生态地球化学循环做出重要贡献。直到最近，只有Chlorobium tepidum的基因组信息可用，Chlorobium tepidum可能是一种来自富含硫化物的温泉的非典型生物。联合基因组研究所（JGI-DOE）已经完成了8个GSB的测序草案，第9个GSB的基因组将于2005年测序。JGI-DOE还将为七种绿球藻的成员制作高质量的序列草案，其中六种是丝状厌氧光养菌（FAP;以前是绿色滑行/非硫细菌）。目前只有一种FAP（橙色绿弯藻）的不完整序列草案可用。最近的研究表明，FAP在生理上是多样的，在自然界中分布广泛。新描述的分离物可以使用不同的途径固定碳、固定氮、氧化硫化物以及可能的二价铁和其他金属。FAP是陆地，淡水和盐水环境中重要但特征不明显的组分，全基因组分析将为其特性提供许多新的见解。目前，许多科学家正在研究光合自养代谢、光合作用的机制和起源以及光合自养生物之间的进化关系。这些问题将在本研究中通过全基因组测序和随后的数据比较生物信息学分析直接解决。由于这将是有史以来为GSB和FAP收集的最大和最全面的数据库，因此本研究中获得的数据将产生非常广泛的影响。完成的序列将存放在公共数据库中，这些数据以及自动和手动注释数据也将通过公开访问的网站提供。 两名博士后科学家和四名本科生研究人员将在执行本研究计划期间接受培训。 PI和Co-PI将为高级本科生和研究生组织一门课程，提供微生物基因组学和生物信息学的被动和主动学习经验。 本课程将填补宾夕法尼亚州立大学微生物学和生物信息学课程的现有空白。