Classification of Myoviridae bacteriophages using protein sequence similarity.
Classification of Myoviridae bacteriophages using protein sequence similarity.
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DOI：
10.1186/1471-2180-9-224
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发表时间：
2009-10-26
期刊：
影响因子：
4.2
通讯作者：
Kropinski AM
中科院分区：
文献类型：
--
作者：
Lavigne R;Darius P;Summer EJ;Seto D;Mahadevan P;Nilsson AS;Ackermann HW;Kropinski AM
我们主张通过整合蛋白质组数据和物理化学参数来统一噬菌体的经典分类和基因组分类。我们之前对Podoviridae全序列成员的这种方法的应用完全支持国际病毒分类委员会(ICTV)目前的噬菌体分类。似乎水平基因转移一般不会完全消除噬菌体之间的进化关系。应用CoreGenes/CoreExtractor蛋白质组比对技术对102个Myoviridae进行比较，发现有3个亚科(Peduovirinae、Teequtrevirinae、Spounavirinae)和8个新的独立属(Bcep781、BcepMu、FelixO1、HAP1、Bzx1、PB1、phiCD119和phiKZ-like病毒)。Peduovirinae亚家族由P2相关噬菌体衍生而来，由两个不同的属组成：“P2样病毒”和“HP1样病毒”。目前，较为复杂的茶树病毒亚科有两个属，即类T4病毒和类KVP40病毒。在类T4病毒属中，有四类病毒具有70%的共同蛋白：T4型、44RR型、RB43型和RB49型。SpounaVirinae含有“SPO1-”和“Twort-like病毒”。这些类群的等级聚类提供了具有生物学意义的亚类，这与我们之前对Podoviridae的分析一致。
We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages. CoreGenes/CoreExtractor proteome comparison techniques applied to 102 Myoviridae suggest the establishment of three subfamilies (Peduovirinae, Teequatrovirinae, the Spounavirinae) and eight new independent genera (Bcep781, BcepMu, FelixO1, HAP1, Bzx1, PB1, phiCD119, and phiKZ-like viruses). The Peduovirinae subfamily, derived from the P2-related phages, is composed of two distinct genera: the "P2-like viruses", and the "HP1-like viruses". At present, the more complex Teequatrovirinae subfamily has two genera, the "T4-like" and "KVP40-like viruses". In the genus "T4-like viruses" proper, four groups sharing >70% proteins are distinguished: T4-type, 44RR-type, RB43-type, and RB49-type viruses. The Spounavirinae contain the "SPO1-"and "Twort-like viruses." The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.
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