Whole Phage Genomics: A Student-based Approach

虽然噬菌体是地球上数量最多的生物实体，对生态、进化和发病机制具有深远的重要性，但对其基因组学的了解远远比不上细菌。德克萨斯A和M大学的Ry Young博士和Carlos Gonzalez博士的这个项目有两个相互依赖的推动力，一个是基础科学，解决了噬菌体基因组学中的这个重大缺陷，另一个是教育学。教育部分是已建立的本科生基因组学计划(PGU)，该计划于2001年在TAMU建立，之前得到了NSF-USDA的支持。科学的重点是注释120个对不同环境细菌属具有感染性的噬菌体基因组：伯克霍尔德氏菌、红球菌、木霉、硫磺弧菌和不动杆菌。选择这些属中每一个属的宿主是因为它们对环境的重要性，即导致植物、动物或人类疾病或造成腐蚀。关于这些不同宿主的噬菌体的基因组信息可能被证明在生物防治策略中有用。噬菌体基因组的比较基因组学还将研究基因组的进化和横向基因转移事件的证据。从环境样本中分离噬菌体并完成和注释噬菌体基因组序列的大部分实验室工作都是由PGU的本科生参与者完成的。PGU的活动包括一门讲授实验室课程--实用基因组学，该课程向生命科学专业的初中生和高年级学生开放。这些课程的学生中有很大一部分是来自代表性不足的少数群体的学生。本课程提供关于噬菌体生物学基础和基因组学基础的讲座，但也侧重于现代高通量DNA测序和基因组注释工具的实用方面。学生们正在进行实验，并在本课程的背景下对噬菌体基因组进行注释。许多学生将准备出版手稿。

Although bacteriophages are the most numerous biological entity on Earth and are profoundly important for ecology, evolution and pathogenesis, far less is known about their genomics than for bacteria. This project by Drs. Ry Young and Carlos Gonzalez of Texas A and M University has two inter-dependent thrusts, one in basic science addressing this significant deficit in phage genomics, and one educational. The educational component is the established Program in Genomics for Undergraduates (PGU), established in 2001 at TAMU with prior NSF-USDA support. The scientific focus is to annotate 120 genomes of bacteriophages infectious for diverse environmental bacterial genera: Burkholderia, Rhodococcus, Xylella, Desulfovibrio, and Acinetobacter. The hosts in each of these genera were selected because of their environmental importance, i.e. causing plant, animal or human disease or causing corrosion. Genomic information about the phage of these various hosts may prove useful in biocontrol strategies. Comparative genomics of the phage genomes will also examine evolution of the genomes and evidence for lateral gene transfer events. Much of the laboratory work isolating phage from environmental samples and completing and annotating the phage genomic sequences is being done by the undergraduate participants of the PGU. The activities of the PGU include a lecture-laboratory course, Practical Genomics, which is open to junior and senior students in the life science majors. A significant fraction of the students in these courses are students from under-represented minority groups. The course provides lectures on the basics of bacteriophage biology and the fundamentals of genomics but also focuses on practical aspects of modern high-throughput DNA sequencing and the tools of genome annotation. The students are conducting the experiments and annotate the phage genomes in the context of this course. Many of the students will prepare manuscripts for publication.