Complete Genome Sequencing of Four Nitrogen-fixing, Plant-associated Burkholderias

该项目将产生四种与植物相关的伯克霍尔德菌属物种的基因组序列：B。sp. PVA5、B. B. tuberum STM-678 T，B. unamae MtI-641 T和B. sp. SRMrh-20。新的DNA测序方法（焦磷酸测序）将用于对这些基因组中的每个基因组的700万个碱基对进行测序。这些数据将被用来编译一个完整的描述基因包含在每一个细菌，然后分析重要的固氮生理机制，并与其他固氮细菌，特别是不同的根瘤菌进行比较。一百多年来，根瘤菌的成员被认为是唯一一组可以固氮（与植物宿主密切相关）和固氮（为植物宿主提供营养）的细菌，这是一个至关重要的过程。因此，发现伯克霍尔德氏菌固氮能力的遗传基础具有强烈的兴趣。一个待测序的菌株，新物种B。tuberum STM-678 T，分离于南非，获得了独立于其他生物的固氮和固氮机制。B。unamae MtI-641 T和B。SRMrh-20代表了与植物相关的固氮菌（来自巴西和墨西哥）的不同进化枝，并且将这些生物放在一起将丰富这些生物的遗传多样性。第四个被测序的菌株，PVA 5（来自巴西），不会通过感染进入根部，可能代表了一种新的共生形式，让我们深入了解这种重要的植物-微生物相互作用的演变。这些与植物相关的伯克霍尔德氏菌也将被检查的基因编码酶的生物控制和土壤修复的途径，通过分解外源性物质。最后，将基因组与其他测序的伯克霍尔德氏菌基因组进行比较，特别是来自致病性物种的基因组，以阐明有毒微生物的进化。这些伯克霍尔德氏菌的测序实现了微生物基因组测序项目的目标，因为生理学家和植物生物学家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NSF感兴趣的许多领域产生影响。一个国际科学家小组（美国，英国，法国、德国、巴西、墨西哥、台湾）一直在研究植物相关伯克霍尔德菌菌株的繁殖、对环境的反应以及与植物的相互作用。 所选的生物体正是实验研究中使用的菌株，因此基因组将对这些研究产生巨大而直接的好处。该项目的一个重要方面将是由相关科学界的一个联合体对DNA序列进行彻底注释。注释过程将是多阶段的：（1）基于初步序列的自动功能评估的早期发布，然后是（2）鼓励其他研究人员参与并贡献其专业知识的社区注释项目。该项目将包括本科生、研究生和博士后参与微生物基因组学和生物信息学的实践培训。此外，加州大学洛杉矶分校是美国种族最多元化的大学之一，并设立了许多项目，向来自代表性不足群体的男女学生介绍科学、技术和数学。在加州大学洛杉矶分校C.A.R.E.的赞助下，许多本科生早在大学二年级就开始从事研究项目。（学术和研究卓越中心），负责监督MARC（少数民族获得研究职业）计划和UC-LEADS（通过高级学位领导）计划，所有这些都是为了帮助来自代表性不足的群体的人追求科学事业而建立的。

This project will produce genome sequences for four plant-associated Burkholderia species: B. sp. PVA5, B. tuberum STM-678T, B. unamae MtI-641T, and B. sp. SRMrh-20. New DNA sequencing methodology (pyrosequencing) will be used to sequence the 7 million base pairs of each of these genomes. These data will be used to compile a complete description of the genes contained in each bacterium, then analyzed for important physiological mechanisms for nitrogen fixation and compared to other nitrogen-fixing bacteria, particularly the phylogenetically distinct rhizobia. For over a hundred years, members of the rhizobia were known as the sole group of bacteria that could nodulate (intimately associate with a plant host) and fix nitrogen (providing nutrients for their plant host), a process of critical importance. Thus it is of intense interest to discover the genetic basis for the nitrogen fixing capacity of the Burkholderia. One strain to be sequenced, the novel species B. tuberum STM-678T, isolated in South Africa, acquired nodulation and nitrogen fixation mechanisms independently from other organisms. B. unamae MtI-641T and B. sp. SRMrh-20 represent different clades of plant associated nodulating nitrogen fixers (from Brazil and Mexico), and taken together these organisms will richly sample the genetic diversity of these organisms. The fourth strain to be sequenced, PVA5 (from Brazil), does not nodulate but enters the root by infection and may represent a new form of symbiosis, giving insight into the evolution of this important plant-microbe interaction. These plant-associated Burkholderia will also be examined for genes encoding enzymes in pathways for biocontrol and for soil remediation via the breakdown of xenobiotics. Lastly, the genomes will be compared to other sequenced Burkholderia genomes, particularly from pathogenic species, in order to shed light on the evolution of virulent microorganisms. The sequencing of these Burkholderia fulfills the goals of the Microbial Genome Sequencing Project because of the community of physiologists and plant 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 interest to the NSF. An international group of scientists (U.S., U.K., France, Germany, Brazil, Mexico,Taiwan) has been researching the plant-associated Burkholderia strains with regard to their phylogeny, their responses to the environment, and their interactions with plants. The selected organisms are the exact strains that are used in the experimental studies, and hence the genome will be of immense and immediate benefit to these pursuits. An important aspect of the project will be the thorough annotation of the DNA sequence, performed by a consortium of the relevant scientific community. The annotation process will be multi-phasic with (1) an early release of automated functional assessments based on preliminary sequence followed by (2) a community annotation project encouraging other researchers to be involved and contribute their expertise. The project will include participation by undergraduate and graduate students and postdocs for hands-on training in microbial genomics and bioinformatics. In addition, UCLA is one of the most ethnically diverse universities in the U.S., and has established many programs to introduce students from under-represented groups, male and female, to science, technology, and mathematics. A number of undergraduate students work on research projects starting as early as their second year in college, under the sponsorship of UCLA C.A.R.E. (Center for Academic and Research Excellence), which oversees the MARC (Minority Access to Research Careers) program, and UC-LEADS (Leadership through Advanced Degrees) programs, all of which have been established to help people from under-represented groups pursue careers in science.