Brandes Nadav, Linial Michal
Einstein Institute of Mathematics, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, Israel.
Department of Biological Chemistry, Room A-530, Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
Biol Direct. 2016 May 21;11:26. doi: 10.1186/s13062-016-0128-3.
Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified evolutionary explanation that accounts for their genome sizes, gene overlapping and capsid properties.
We performed an unbiased statistical analysis of ~100 families within ~400 genera that comprise the currently known viral world. We found that the volume utilization of capsids is often low, and greatly varies among viral families. Furthermore, although viruses span three orders of magnitude in genome length, they almost never have over 1500 overlapping nucleotides, or over four significantly overlapping genes per virus.
Our findings undermine the generality of the compression theory, which emphasizes optimal packing and length dependency to explain overlapping genes and capsid size in viral genomes. Instead, we propose that gene novelty and evolution exploration offer better explanations to size constraints and gene overlapping in all viruses.
This article was reviewed by Arne Elofsson and David Kreil.
病毒是最简单的复制单元，其特点是编码基因数量有限且重叠基因的比例极高。我们寻求一种统一的进化解释，以说明它们的基因组大小、基因重叠和衣壳特性。
我们对构成当前已知病毒世界的约400个属中的约100个科进行了无偏统计分析。我们发现衣壳的体积利用率通常较低，并且在病毒科之间差异很大。此外，尽管病毒的基因组长度跨越三个数量级，但它们几乎从未有超过1500个重叠核苷酸，或每个病毒超过四个显著重叠的基因。
我们的发现削弱了压缩理论的普遍性，该理论强调最佳包装和长度依赖性来解释病毒基因组中的重叠基因和衣壳大小。相反，我们提出基因新颖性和进化探索能更好地解释所有病毒的大小限制和基因重叠。
本文由阿恩·埃洛夫松（Arne Elofsson）和大卫·克雷尔（David Kreil）评审。
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