Complete Genome Sequencing of the Chromatically Adapting Cyanobacterium Fremyella diplosiphon

该项目将产生淡水丝状蓝藻freremyella diplosiphon UTEX 481的基因组序列。新的DNA测序方法（焦磷酸测序）将用于对该基因组的1200万个碱基对进行测序，该基因组是已知细菌中最大的基因组之一。这些数据将用于编制该细菌中所含基因的完整描述，以揭示原核生物对环境光颜色变化的反应的重要生理和调节机制。遗传内容也将与其他测序的蓝藻物种和光合细菌进行比较，以提供光合作用和蓝藻物种进化的广阔图景。F. diplosiphon是一种发育良好的模式生物，大约四十年来一直用于促进对微生物如何感知和响应其环境的理解。最初选择和培养的是它对环境光色条件变化的感知和反应能力，它的光合作用光收集触角对光色变化的反应现在是所有生物中最了解的。F. diplosiphon用于研究广泛的其他生理和生化过程，如“蛋白质组重塑”，以应对营养限制。它还用于研究发育反应，如气泡形成和向光性，生物体在单侧施加光的存在或不存在的情况下向特定方向生长的能力。重要的生化过程，包括叶绿素和胆磷脂的生物合成，也在该物种中被研究，F. diplosiphon是少数在植物和动物的信号转导中同时产生cAMP和cGMP的原核生物之一，这是关键的信号分子。diplosiphon的测序实现了微生物基因组测序计划的目标，因为生理学家和发育生物学家社区将从序列数据中受益，并参与其分析，公开发布序列和基因预测，以及这项工作将对基础生物学的许多领域产生影响。光响应在光合作用过程中非常重要，而光合作用在地球的进化中起着至关重要的作用，并且对几乎所有生态系统的维持都是必要的。此外，对这些生理过程的理解有助于生物能源的开发。该项目的一个重要方面将是DNA序列的全面注释，由相关科学界的一个联盟执行。这将涉及硕士和博士研究生和博士后研究员，并将提供使用生物信息学方法来操作和注释微生物基因组的重要培训。这项活动还将用于美国至少三个实验室的基因组学本科培训和斯坦福大学的一门本科课程。最后，印第安纳州布卢明顿市的高中生将通过一个扩展项目学习基因组结构和功能的基础知识，该项目将把这些信息带到他们的课堂上。

This project will produce a genome sequence of the fresh-water filamentous cyanobacterium Fremyella diplosiphon UTEX 481. New DNA sequencing methodology (pyrosequencing) will be used to sequence the 12 million base pairs of this genome, one of the largest known in bacteria. These data will be used to compile a complete description of the genes contained in this bacterium, to reveal important physiological and regulatory mechanisms involved in prokaryotic responses to changes in ambient light color. The genetic content will also be compared to other sequenced cyanobacterial species and photosynthetic bacteria, to provide a broad picture of the evolution of photosynthesis and the cyanobacterial species. F. diplosiphon is a well-developed model organism that for some forty years has been used to advance understanding of how microorganisms sense and respond to their environment. Initially selected and cultivated for its ability to sense and respond to changes in ambient light color conditions, the response of its photosynthetic light harvesting antennae to light color changes is now the best understood of any organism. F. diplosiphon is used to study a wide range of additional physiological and biochemical processes such as "proteome remodeling" in response to nutrient limitation. It is also used to study developmental responses such as gas vesicle formation and phototropism, the ability of an organism to grow in a specific direction in response to the presence or absence of unilaterally applied light. Important biochemical processes, including chlorophyll and bilin biosynthesis, are also studied in this species, and F. diplosiphon is one of the few prokaryotes that produces both cAMP and cGMP in signal transduction, key signalling molecules in plants and animals. The sequencing of F. diplosiphon fulfills the goals of the Microbial Genome Sequencing Project because of the community of physiologists and developmental biologists who will benefit from the sequence data, and participate in its analysis, the public release of the sequence and gene predictions, and the impact this work will have on many areas of fundamental biology. Light responses are important in the process of photosynthesis, which played a critical role in the evolution of our planet, and are necessary for the maintenance of nearly every ecosystem. Moreover an understanding of these physiological processes can contribute to the development of bioenergy sources. An important aspect of the project will be the thorough annotation of the DNA sequence, performed by a consortium of the relevant scientific community. This will involve Masters and Ph.D. students and postdoctoral fellows, and will provide significant training in the use of bioinformatics approaches for manipulating and annotating microbial genomes. This activity will also be used for undergraduate training in genomics in at least three laboratories in the United States and in one undergraduate course at Stanford University. Finally, high school students in Bloomington, Indiana will learn the basics of genome structure and function through an outreach program that will bring this information to their classes.