Microbial Genome Sequencing: Algal Virus Genomics

马萨诸塞大学(Lowell)的Michael Graves博士和内布拉斯加大学(林肯)的James Van Etten博士获得了一项赠款，用于对4种遗传多样性病毒的基因组进行测序，这些病毒感染世界各地淡水环境中发现的某些单细胞、真核、类小球藻的绿藻。小球藻病毒基因组非常大，其中一个分离株PBCV-1(基因组大小=330,744 bp dsDNA)编码11个tRNA和~375个蛋白质，其中近一半与已知功能的蛋白质相似。这些基因中的许多编码与病毒很少相关的蛋白质(例如DNA限制性内切酶和参与蛋白质糖基化的酶)。PBCV-1与其他小球藻病毒的比较表明，它们非常不同；小球藻病毒的整个“基因库”超过了375个PBCV-1编码的基因。因此，单个分离株的序列并不能给出全部情况，在众多的分离株中有许多新的基因等待发现。小球藻病毒基因组的大小(300kbp)与细菌人工染色体(BAC)相当，因此将采用鸟枪式亚克隆和测序BAC的技术。此外，小球藻病毒基因组包含的重复序列很少，并且它们的基因密集排列，因此每个读取的序列都至少包含一个基因的部分。目前，对藻类病毒的研究还处于初级阶段。藻类在水环境中发挥着重要作用，而藻类病毒在调节藻类群落方面发挥着重要的作用，尽管人们对此知之甚少，例如破坏有毒的藻类水华，如那些导致赤潮和赤潮的藻类。因此，藻类病毒的研究对于更好地了解水环境的动态是至关重要的。从这项研究中获得的知识将有助于推进藻类病毒学和这些病毒在其环境中所扮演的角色的研究。虽然小球藻病毒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的是多么的少。毫无疑问，更多小球藻病毒的基因组序列将识别编码既具有科学意义又可能具有商业价值的蛋白质的新基因。最后，从这项研究中获得的信息将推动对进化史的研究，不仅是所有藻类病毒的进化史，也包括其他大型dsDNA病毒家族的进化史，如痘病毒和疱疹病毒。

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.