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

该项目将产生四种植物相关伯克氏菌的基因组序列：B. sp. PVA5、B. tuberum STM-678T、B. unamae MtI-641T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的700万个碱基对进行测序。这些数据将用于编制每个细菌中所含基因的完整描述，然后分析固氮的重要生理机制，并与其他固氮细菌，特别是系统发育上不同的根瘤菌进行比较。一百多年来，根瘤菌被认为是唯一一组可以结瘤（与植物宿主密切相关）和固定氮（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，发现伯克氏菌固氮能力的遗传基础是非常有趣的。其中一个待测序的菌株是在南非分离到的新物种B. tuberum STM-678T，它独立于其他生物获得结瘤和固氮机制。B. unamae MtI-641T和B. sp. SRMrh-20代表了植物相关结瘤固氮菌的不同分支（来自巴西和墨西哥），将这些生物结合在一起将丰富这些生物的遗传多样性样本。第四种被测序的菌株，PVA5（来自巴西），不结瘤，但通过感染进入根部，可能代表一种新的共生形式，使我们深入了解这种重要的植物-微生物相互作用的进化。这些与植物相关的伯克霍尔德菌也将被检查在生物防治途径中编码酶的基因和通过分解外源物质进行土壤修复的基因。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，特别是来自致病物种的基因组，以便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计划的目标，因为生理学家和植物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，以及这项工作将对美国国家科学基金会感兴趣的许多领域产生影响。一个由美国、英国、法国、德国、巴西、墨西哥和台湾科学家组成的国际研究小组一直在研究植物相关的伯克霍尔德菌菌株的系统发育、对环境的反应以及它们与植物的相互作用。所选择的生物是实验研究中使用的确切菌株，因此基因组将对这些研究有巨大而直接的好处。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。注释过程将分为多个阶段：(1)基于初步序列的自动化功能评估的早期发布，然后(2)鼓励其他研究人员参与并贡献他们的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最具种族多样性的大学之一，并建立了许多项目，将学生从代表性不足的群体（男性和女性）引入科学，技术和数学。在加州大学洛杉矶分校卓越学术与研究中心的赞助下，许多本科生早在大学二年级就开始从事研究项目，该中心负责监督MARC（少数族裔获得研究职业）计划和UC-LEADS（高级学位领导力）计划，所有这些计划都是为了帮助弱势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.