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Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication

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...

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Autores principales: Kong, Sing-Guan, Fan, Wen-Lang, Chen, Hong-Da, Hsu, Zi-Ting, Zhou, Nengji, Zheng, Bo, Lee, Hoong-Chien
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771390/
https://www.ncbi.nlm.nih.gov/pubmed/19898631
http://dx.doi.org/10.1371/journal.pone.0007553
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author Kong, Sing-Guan
Fan, Wen-Lang
Chen, Hong-Da
Hsu, Zi-Ting
Zhou, Nengji
Zheng, Bo
Lee, Hoong-Chien
author_facet Kong, Sing-Guan
Fan, Wen-Lang
Chen, Hong-Da
Hsu, Zi-Ting
Zhou, Nengji
Zheng, Bo
Lee, Hoong-Chien
author_sort Kong, Sing-Guan
collection PubMed
description 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 [Image: see text]-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.
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spelling pubmed-27713902009-11-09 Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication Kong, Sing-Guan Fan, Wen-Lang Chen, Hong-Da Hsu, Zi-Ting Zhou, Nengji Zheng, Bo Lee, Hoong-Chien PLoS One Research Article 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 [Image: see text]-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. Public Library of Science 2009-11-09 /pmc/articles/PMC2771390/ /pubmed/19898631 http://dx.doi.org/10.1371/journal.pone.0007553 Text en Kong et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Kong, Sing-Guan
Fan, Wen-Lang
Chen, Hong-Da
Hsu, Zi-Ting
Zhou, Nengji
Zheng, Bo
Lee, Hoong-Chien
Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication
title Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication
title_full Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication
title_fullStr Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication
title_full_unstemmed Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication
title_short Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication
title_sort inverse symmetry in complete genomes and whole-genome inverse duplication
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771390/
https://www.ncbi.nlm.nih.gov/pubmed/19898631
http://dx.doi.org/10.1371/journal.pone.0007553
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