A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)
A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)
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DOI：
10.1007/s00705-012-1601-7
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发表时间：
2013-06-01
影响因子：
2.7
通讯作者：
Varsani, Arvind
中科院分区：
文献类型：
--
作者：
Muhire, Brejnev;Martin, Darren P.;Varsani, Arvind
小环状单链DNA病毒基因组的扩增、克隆和测序的便捷性方面的最新进展，大大加快了将乳房病毒（双侧病毒科，乳房病毒属）全基因组序列存入公共序列数据库的速度。尽管目前存在对新确定的完整的乳腺炎病毒基因组序列进行种级分类的指南，但这些指南很难应用于大型序列数据集，而且足够宽松，实际上为提出新物种和毒株存在很大的余地。由于缺乏一种标准化和严格的方法来测试一个新的基因组序列是否值得这样的分类，导致越来越多的可疑的mastovirus物种建议。重要的是，当前指南中推荐的序列比对和两两同一性计算方案可以很容易地进行修改，以使新确定的mastrevirus基因组序列的分类更加客观。在这里，我们提出了这些协议的修改版本，这些版本应该大大减少当前系统允许的分类不一致的程度。为了促进这些指南在mastrevirus物种划分中的客观应用，我们还提供了一个用户友好的计算机程序，SDT（物种划分工具），用于计算和图形显示成对基因组身份评分。我们将SDT应用于2012年5月公开的939个乳头状病毒全基因组序列，并基于我们的方案获得的配对识别分数分布，我们提出了乳头状病毒种和品系划分阈值分别为> 78%和> 94%识别度。
Recent advances in the ease with which the genomes of small circular single-stranded DNA viruses can be amplified, cloned, and sequenced have greatly accelerated the rate at which full genome sequences of mastreviruses (family Geminiviridae, genus Mastrevirus) are being deposited in public sequence databases. Although guidelines currently exist for species-level classification of newly determined, complete mastrevirus genome sequences, these are difficult to apply to large sequence datasets and are permissive enough that, effectively, a high degree of leeway exists for the proposal of new species and strains. The lack of a standardised and rigorous method for testing whether a new genome sequence deserves such a classification is resulting in increasing numbers of questionable mastrevirus species proposals. Importantly, the recommended sequence alignment and pairwise identity calculation protocols of the current guidelines could easily be modified to make the classification of newly determined mastrevirus genome sequences significantly more objective. Here, we propose modified versions of these protocols that should substantially minimise the degree of classification inconsistency that is permissible under the current system. To facilitate the objective application of these guidelines for mastrevirus species demarcation, we additionally present a user-friendly computer program, SDT (species demarcation tool), for calculating and graphically displaying pairwise genome identity scores. We apply SDT to the 939 full genome sequences of mastreviruses that were publically available in May 2012, and based on the distribution of pairwise identity scores yielded by our protocol, we propose mastrevirus species and strain demarcation thresholds of > 78 % and > 94 % identity, respectively.