Microbial Genome Sequencing: Algal Virus Genomics

马萨诸塞州大学（洛厄尔）的迈克尔·格雷夫斯博士和内布拉斯加大学（林肯）的詹姆斯·货车·埃滕博士获得了一笔赠款，用于对感染世界各地淡水环境中某些单细胞、真核、类绿藻绿色藻类的4种遗传多样性病毒的基因组进行测序。该病毒的基因组非常大;一个分离株PBCV-1（基因组大小= 330，744 bp dsDNA）编码11个tRNA和约375种蛋白质，其中近一半类似于已知功能的蛋白质。 这些基因中的许多编码很少与病毒相关的蛋白质（例如DNA限制性内切酶和参与蛋白质糖基化的酶）。PBCV-1和其他雷氏杆菌病毒之间的比较表明它们非常多样化;雷氏杆菌病毒的整个“基因库”超过了375个PBCV-1编码的基因。因此，单个分离株的序列不能给出全貌，许多新基因等待在众多分离株中发现。该病毒基因组的大小（300 kbp）与细菌人工染色体（BAC）相当，因此将采用为鸟枪亚克隆和测序BAC开发的技术。另外，藻类病毒基因组中重复序列少，基因密集，因此每一个序列都至少包含一个基因的一部分。目前，藻类病毒的研究还处于起步阶段。藻类在水生环境中发挥着重要作用，藻类病毒在调节藻类群落方面发挥着重要作用，尽管人们对此知之甚少，例如破坏有毒藻类水华，如造成赤潮和褐潮的藻类水华。因此，藻类病毒的研究对于更好地了解水环境的动态至关重要。从这项研究中获得的知识将有助于推进藻类病毒学以及这些病毒在其环境中所发挥的作用的研究。虽然藻类病毒PBCV-1的序列增加了我们对大型dsDNA藻类病毒基因组结构的了解，但它也揭示了我们所知甚少。毫无疑问，更多的雷氏杆菌病毒的基因组序列将确定编码蛋白质的新基因，这些蛋白质既有科学意义，也可能具有商业价值。最后，从这项研究中获得的信息将推进进化历史的研究，不仅是所有藻类病毒，而且是其他大dsDNA病毒家族，如痘病毒和疱疹病毒的进化历史。

A grant has been awarded to Drs. Michael Graves of the University of Massachusetts (Lowell) and James Van Etten of the University of Nebraska (Lincoln) to sequence the genomes of 4 genetically diverse viruses that infect certain unicellular, eukaryotic, chlorella-like green algae found in freshwater environments worldwide. The chlorella virus genomes are very large; one isolate, PBCV-1, (genome size = 330,744 bp dsDNA) codes for 11 tRNAs and ~375 proteins, nearly half of which resemble proteins of known function. Many of these genes encode proteins (e.g. DNA restriction endonucleases and enzymes involved in protein glycosylation) rarely associated with viruses. Comparisons between PBCV-1 and other chlorella viruses indicate they are very diverse; the entire "gene pool" of the chlorella viruses exceeds the 375 PBCV-1-encoded genes. Therefore, the sequence of a single isolate does not give the total picture and many new genes await discovery among the numerous isolates. The sizes of the chlorella virus genomes ( 300 kbp) are comparable to bacterial artificial chromosomes (BACs) and therefore technologies developed for shotgun subcloning and sequencing BACs will be employed. Additionally, chlorella virus genomes contain little repetitive sequence and their genes are densely packed; therefore, every sequence read will contain at least part of a gene.At present, the study of algal viruses is in its infancy. Algae play an important role in aquatic environments and algal viruses play a significant, albeit poorly understood, role in regulating algal communities, e.g. destroying toxic algal blooms such as those responsible for red tides and brown tides. Therefore, the study of algal viruses is critical to a better understanding of the dynamics of aquatic environments. The knowledge gained from this study will help to advance the study of algal virology and the roles these viruses play in their environment. While the sequence of chlorella virus PBCV-1 led to an increase in our knowledge of the genome structure of large dsDNA algal viruses, it also revealed how little we know. Undoubtedly, the genomic sequences of additional chlorella viruses will identify new genes that encode proteins that are both scientifically interesting and may have commercial value. Finally, the information gained from this research will advance the study of the evolutionary history, not only of all algal viruses, but also the evolutionary histories of the other families of large dsDNA viruses such as the pox viruses and herpes viruses.