Microbial Genome Sequencing: Phages of Agronomic Bacteria: A Student Based Genomics Approach

一个由NSF资助的基于本科生的噬菌体基因组学项目已经开发出来。 细菌病毒，或噬菌体，是迄今为止地球上数量最多的生物实体，在所有环境中的细菌生态学中起着主导作用。 此外，细菌病原体对植物和动物（包括人类）的毒力通常由噬菌体决定和传播。 噬菌体基因组学是唯一适合介绍大学生到真实的研究有几个原因。 噬菌体基因组足够小，一个本科团队可以在一个学期的实验室工作中实现足够的“鸟枪”序列覆盖和初步注释。 此外，微生物和真核生物基因组计划所需的高通量在噬菌体基因组学中的价值较小。 这部分是由于基因组的仔细手动注释的必要性，这些基因组密集在相对较小的基因中，这些基因通常与任何数据库条目无关。 在这个过程中，学生将深入了解从基因结构到病毒生物学的重要概念。 具体的科学目标是测序15个不同的，有毒的噬菌体基因组的农学和临床上重要的土壤细菌，洋葱伯克霍尔德氏菌复合体（BCC）。 除了基于生物信息学的注释，学生将通过病毒体的质谱分析来识别结构蛋白基因。 此外，将确定线性dsDNA基因组末端的结构。 学生将进行实验，以确定宿主范围，后代爆发大小和裂解基因表征。 除了生成具有科学重要性的数据外，噬菌体基因组学项目的本科生一直表示，这是一种独特而强大的方式，可以告知他们科学是否是一个真实的职业选择。将建立一个网站，描述课程的组织结构，所采用的实验方案和噬菌体测序的注释。

An NSF-funded program of undergraduate-based bacteriophage genomics has been developed. Bacterial viruses, or bacteriophages, are by far the most numerous biological entities on the planet and play a dominant role in the ecology of bacteria in all environments. Moreover, the virulence of bacterial pathogens for plants and animals, including humans, is often determined and transmitted by bacteriophages. Bacteriophage genomics is uniquely suited for introducing undergraduates to real research for several reasons. Bacteriophage genomes are small enough for an undergraduate team to achieve sufficient "shotgun" sequence coverage and preliminary annotation in a semester's laboratory effort. Moreover, the high-throughput necessary for microbial and eukaryotic genome projects is of less value in phage genomics. This is due in part to the necessity for careful manual annotation of the genomes, which are dense in relatively small genes that are frequently unrelated to any database entries. In this process, students achieve an in-depth immersion into important concepts from gene structure to viral biology. The specific scientific goal is to sequence 15 diverse, virulent bacteriophage genomes of the agronomically and clinically important group of soil bacteria, the Burkholderia cepacia complex (BCC). In addition to bioinformatics-based annotations, students will identify structural protein genes through mass spectrometry analysis of virions. Also, the structure of the linear dsDNA genomic termini will be determined. Students will perform experiments to determine host range, progeny burst size and lysis gene characterization. In addition to generating data of scientific importance, the undergraduates in the bacteriophage genomics program have consistently indicated that it is a unique and powerful way to inform and empower them as to whether science is a real career option. A web site describing the organizational structure of the course, the experimental protocols that are employed and the annotation of the sequenced bacteriophage will be established.