Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size.
Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene size.
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DOI：
10.1016/j.jmb.2010.01.011
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发表时间：
2010-03-19
影响因子：
5.6
通讯作者：
Hendrix RW
中科院分区：
文献类型：
--
作者：
Hatfull GF;Jacobs-Sera D;Lawrence JG;Pope WH;Russell DA;Ko CC;Weber RJ;Patel MC;Germane KL;Edgar RH;Hoyte NN;Bowman CA;Tantoco AT;Paladin EC;Myers MS;Smith AL;Grace MS;Pham TT;O'Brien MB;Vogelsberger AM;Hryckowian AJ;Wynalek JL;Donis-Keller H;Bogel MW;Peebles CL;Cresawn SG;Hendrix RW
分枝杆菌噬菌体是感染分枝杆菌宿主的病毒。将已测序的噬菌体基因组扩展至总共 60 个（全部感染共同的细菌宿主），可以进一步了解其多样性和进化。在60个噬菌体基因组中，55个可以根据其核苷酸序列相似性分为9个簇，其中5个可以进一步分为亚簇；五个基因组不与其他噬菌体聚集。簇内基因组之间的序列多样性差异很大；例如，簇 D 中的 6 个基因组彼此之间的平均核苷酸相似性超过 97.5%。相比之下，通过对角图分析几乎无法检测到簇 I 中两个基因组之间的相似性。总共 6,858 个预测的 ORF 被分为 1523 个相关序列的家族 (phams)，其中 46% 仅拥有一个成员。只有 18.8% 的 pham 与非分枝杆菌噬菌体数据库条目具有序列相似性，并且不到 10% 的 pham 可以根据数据库搜索或同线性分配功能。基因组聚类有助于识别处于最大遗传通量并且更有可能在相对较新的进化时间内水平交换的基因。尽管分枝杆菌噬菌体基因表现出比宿主基因更小的平均大小（205 个残基与 315 个残基），但较高通量的噬菌体基因平均只有 ∼100 个氨基酸，这表明遗传交换的主要单位对应于单个蛋白质结构域。
Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of sixty – all infecting a common bacterial host – provides further insight into their diversity and evolution. Of the sixty phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, five of which can be further divided into subclusters; five genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the six genomes in cluster D share more than 97.5% average nucleotide similarity with each other. In contrast, similarity between the two genomes in Cluster I is barely detectable by diagonal plot analysis. The total of 6,858 predicted ORFs have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit smaller average size than genes of their host (205 residues compared to 315), phage genes in higher flux average only ∼100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains.
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影响因子：
9.2
作者：
Hendrix, RW
通讯作者：
Hendrix, RW
影响因子：
5.6
作者：
Casjens, S;Winn-Stapley, DA;Clark, AJ
通讯作者：
Clark, AJ
影响因子：
5.6
作者：
Clark, AJ;Inwood, W;Dhillon, TS
通讯作者：
Dhillon, TS
影响因子：
2.6
作者：
Casjens, Sherwood R.
通讯作者：
Casjens, Sherwood R.
DOI：
10.1007/978-1-60327-565-1_7
发表时间：
2009
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Casjens, Sherwood R;Gilcrease, Eddie B
通讯作者：
Gilcrease, Eddie B