Evaluation of the Persistence of Higher-Order Strand Symmetry in Genomic Sequences by Novel Word Symmetry Distance Analysis

• Main Authors: Bi Huang, Li-Fang Huang, Shang-Hong Zhang
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2019-03-01
• Series: Frontiers in Genetics
• Subjects: the second parity rule; higher-order oligonucleotide; whole-genome sequences; frequency analysis; word symmetry distance (WSD)
• Online Access: https://www.frontiersin.org/article/10.3389/fgene.2019.00148/full

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.