Huang Bi, Huang Li-Fang, Zhang Shang-Hong
Key Laboratory of Gene Engineering of Ministry of Education, Biotechnology Research Center, Sun Yat-sen University, Guangzhou, China.
Front Genet. 2019 Mar 7;10:148. doi: 10.3389/fgene.2019.00148. eCollection 2019.
For the ubiquitous phenomenon of strand symmetry, it has been shown that it may persist for higher-order oligonucleotides. However, there is no consensus about to what extent (order of oligonucleotides or length of words) strand symmetry still persists. To determine the extent of strand symmetry in genomic sequences is critically important for the further understanding of the phenomenon. Based on previous studies, we have developed an algorithm for the novel word symmetry distance analysis. We applied it to evaluate the higher-order strand symmetry for 206 archaeal genomes and 2,659 bacterial genomes. Our results show that the new approach could provide a clear-cut criterion to determine the extent of strand symmetry for a group of genomes or individual genomes. According to the new measure, strand symmetry would tend to persist for up to 8-mers in archaeal genomes, and up to 9-mers in bacterial genomes. And the persistence may vary from 6- to 9-mers in individual genomes. Moreover, higher-order strand symmetry would tend to positively correlate with GC content and mononucleotide symmetry levels of genomic sequences. The variations of higher-order strand symmetry among genomes would indicate that strand symmetry itself may not be strictly relevant to biological functions, which would provide some insights into the origin and evolution of the phenomenon.
对于普遍存在的链对称性现象，已有研究表明其可能在高阶寡核苷酸中持续存在。然而，对于链对称性在何种程度上（寡核苷酸的阶数或词的长度）仍然存在，尚无共识。确定基因组序列中链对称性的程度对于进一步理解该现象至关重要。基于先前的研究，我们开发了一种用于新颖词对称性距离分析的算法。我们将其应用于评估206个古菌基因组和2659个细菌基因组的高阶链对称性。我们的结果表明，新方法可以提供一个明确的标准来确定一组基因组或单个基因组中链对称性的程度。根据新的度量标准，链对称性在古菌基因组中倾向于在长达8聚体时持续存在，在细菌基因组中则长达9聚体。并且在单个基因组中，这种持续性可能在6至9聚体之间变化。此外，高阶链对称性倾向于与基因组序列的GC含量和单核苷酸对称性水平呈正相关。基因组之间高阶链对称性的变化表明，链对称性本身可能与生物学功能没有严格的相关性，这将为该现象的起源和进化提供一些见解。
