title: Conservation vs. variation of dinucleotide frequencies across bacterial and archaeal genomes: evolutionary implications.
abstract: During the long history of biological evolution, genome structures have undergone enormous changes. Nevertheless, some traits or vestiges of the primordial genome (defined as the most primitive nucleic acid genome for life on earth in this paper) may remain in modern genetic systems. It is of great importance to find these traits or vestiges for the study of the origin and evolution of genomes. As the shorter is a sequence, the less probable it would be modified during genome evolution. And if mutated, it would be easier to reappear at the same site or another site. Consequently, the genomic frequencies of very short nucleotide sequences, such as dinucleotides, would have considerable chances to be conserved during billions of years of evolution. Prokaryotic genomes are very diverse and with a wide range of GC content. Therefore, in order to find traits or vestiges of the primordial genome remained in modern genetic systems, we have studied the characteristics of dinucleotide frequencies across bacterial and archaeal genomes. We analyzed the dinucleotide frequency patterns of the whole-genome sequences from more than 1300 prokaryotic species (bacterial and archaeal genomes available as of December 2012). The results show that the frequencies of the dinucleotides AC, AG, CA, CT, GA, GT, TC, and TG are well-conserved across various genomes, while the frequencies of other dinucleotides vary considerably among species. The dinucleotide frequency conservation/variation pattern seems to correlate with the distributions of dinucleotides throughout a genome and across genomes. Further analysis indicates that the phenomenon would be determined by strand symmetry of genomic sequences (the second parity rule) and GC content variations among genomes. We discussed some possible origins of strand symmetry. And we propose that the phenomenon of frequency conservation of some dinucleotides may provide insights into the genomic composition of the primordial genetic system.
authors.affiliation: Key Laboratory of Gene Engineering of Ministry of Education, and Biotechnology Research Center, Sun Yat-sen University Guangzhou, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Zhang
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.forename: Hong-Sheng
authors.initials: HS
authors.lastname: Zhong
authors.forename: Shang-Hong
authors.initials: SH
authors.lastname: Zhang
keywords: GC content; compositional analysis; dinucleotide frequency; origin and evolution of genomes; primordial genome; strand symmetry; whole-genome sequences
references.citation: Nucleic Acids Res. 1984 Feb 10;12(3):1749-63
references.pmid: 6583663
references.citation: Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12837-41
references.pmid: 7809131
references.citation: Bioinformatics. 2002 Aug;18(8):1021-33
references.pmid: 12176825
references.citation: Comput Appl Biosci. 1991 Jan;7(1):39-49
references.pmid: 2004273
references.citation: Nucleic Acids Res. 1980 Oct 10;8(19):4545-62
references.pmid: 7433114
references.citation: Front Microbiol. 2013 Sep 06;4:269
references.pmid: 24046767
references.citation: Bioinformatics. 2001 Jun;17(6):557-9
references.pmid: 11395434
references.citation: J Mol Evol. 1995 Nov;41(5):573-81
references.pmid: 7490771
references.citation: Mol Biol Evol. 1999 Jun;16(6):719-23
references.pmid: 10368950
references.citation: Bioinformatics. 2010 Feb 15;26(4):478-85
references.pmid: 20031973
references.citation: Proc Natl Acad Sci U S A. 1962 Apr 15;48:582-92
references.pmid: 13918161
references.citation: Nucleic Acids Res. 1993 Jun 25;21(12):2797-800
references.pmid: 8332488
references.citation: BMC Res Notes. 2012 Nov 17;5:639
references.pmid: 23158698
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17828-33
references.pmid: 17093051
references.citation: J Theor Biol. 1982 Apr 21;95(4):783-91
references.pmid: 6287118
references.citation: Trends Genet. 1995 Jul;11(7):283-90
references.pmid: 7482779
references.citation: Mol Biol Evol. 1995 Sep;12(5):949-58
references.pmid: 7476142
references.citation: J Exp Zool. 2000 Apr 15;288(1):21-2
references.pmid: 10750049
references.citation: Gene. 2000 Dec 30;261(1):127-37
references.pmid: 11164044
references.citation: Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1358-62
references.pmid: 1741388
references.citation: J Mol Evol. 1991 Jan;32(1):24-30
references.pmid: 1901365
references.citation: Genomics. 1992 Aug;13(4):1056-64
references.pmid: 1505943
references.citation: Genomics. 2011 May;97(5):330-1
references.pmid: 21324351
references.citation: Biochem Biophys Res Commun. 2002 Nov 22;299(1):126-34
references.pmid: 12435398
references.citation: J Theor Biol. 1999 Nov 21;201(2):141-56
references.pmid: 10556022
references.citation: J Bacteriol. 1997 Jun;179(12):3899-913
references.pmid: 9190805
references.citation: J Biol Chem. 1981 Aug 25;256(16):8458-62
references.pmid: 6943145
references.citation: Curr Issues Mol Biol. 2013;15:19-24
references.pmid: 22772895