生物圈的暗物质：噬菌体多样性的奇妙世界
Dark Matter of the Biosphere: the Amazing World of Bacteriophage Diversity.
作者信息
Hatfull Graham F
机构信息
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
出版信息
J Virol. 2015 Aug;89(16):8107-10. doi: 10.1128/JVI.01340-15. Epub 2015 May 27.
Abstract
Bacteriophages are the most abundant biological entities in the biosphere, and this dynamic and old population is, not surprisingly, highly diverse genetically. Relative to bacterial genomics, phage genomics has advanced slowly, and a higher-resolution picture of the phagosphere is only just emerging. This view reveals substantial diversity even among phages known to infect a common host strain, but the relationships are complex, with mosaic genomic architectures generated by illegitimate recombination over a long period of evolutionary history.
摘要
噬菌体是生物圈中数量最为丰富的生物实体，这个充满活力且古老的群体在基因上高度多样也就不足为奇了。相对于细菌基因组学，噬菌体基因组学发展缓慢，而对噬菌体圈的更高分辨率图景才刚刚浮现。这一图景揭示了即使在已知感染同一宿主菌株的噬菌体之间也存在着巨大的多样性，但它们之间的关系很复杂，在漫长的进化历史中通过非法重组产生了镶嵌式基因组结构。
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Virology. 2014 Nov;468-470:421-443. doi: 10.1016/j.virol.2014.08.024.
4
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.
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mBio. 2014 Feb 4;5(1):e01051-13. doi: 10.1128/mBio.01051-13.
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Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles.
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