title: Inverse symmetry in complete genomes and whole-genome inverse duplication.
abstract: The cause of symmetry is usually subtle, and its study often leads to a deeper understanding of the bearer of the symmetry. To gain insight into the dynamics driving the growth and evolution of genomes, we conducted a comprehensive study of textual symmetries in 786 complete chromosomes. We focused on symmetry based on our belief that, in spite of their extreme diversity, genomes must share common dynamical principles and mechanisms that drive their growth and evolution, and that the most robust footprints of such dynamics are symmetry related. We found that while complement and reverse symmetries are essentially absent in genomic sequences, inverse-complement plus reverse-symmetry is prevalent in complex patterns in most chromosomes, a vast majority of which have near maximum global inverse symmetry. We also discovered relations that can quantitatively account for the long observed but unexplained phenomenon of -mer skews in genomes. Our results suggest segmental and whole-genome inverse duplications are important mechanisms in genome growth and evolution, probably because they are efficient means by which the genome can exploit its double-stranded structure to enrich its code-inventory.
authors.affiliation: Graduate Institute of Systems Biology and Bioinformatics, National Central University, Chungli, Taiwan, Republic of China.
authors.forename: Sing-Guan
authors.initials: SG
authors.lastname: Kong
authors.forename: Wen-Lang
authors.initials: WL
authors.lastname: Fan
authors.forename: Hong-Da
authors.initials: HD
authors.lastname: Chen
authors.forename: Zi-Ting
authors.initials: ZT
authors.lastname: Hsu
authors.forename: Nengji
authors.initials: N
authors.lastname: Zhou
authors.forename: Bo
authors.initials: B
authors.lastname: Zheng
authors.forename: Hoong-Chien
authors.initials: HC
authors.lastname: Lee
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D002875:Chromosomes / Q000648:ultrastructure; D003062:Codon; D019295:Computational Biology / Q000379:methods*; D004330:Drosophila / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D012984:Software
chemical_list: D003062:Codon