| [1] Kornberg A, Baker TA. DNA Replication. 2nd ed. New York: WH Freeman and Company, 1992.[2] Rocha EPC. The replication-related organization of bacterial genomes. Microbiology, 2004, 150(6): 1609-1627.[3] Rocha EPC. The organization of the bacterial genome. Annu Rev Genet, 2008, 42: 211-233.[4] Arakawa K, Suzuki H, Tomita M. Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index. BMC Genomics, 2009, 10: 640.[5] Lind PA, Andersson DI. Whole-genome mutational biases in bacteria. Proc Natl Acad Sci USA, 2008, 105(46): 17878-17883.[6] Frank AC, Lobry JR. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene, 1999, 238(1): 65-77.[7] Mrázek J, Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA, 1998, 95(7): 3720-3725.[8] Lobry JR. Origin of replication of Mycoplasma genitalium. Science, 1996, 272(5262): 745-746.[9] Watson JD, Crick FCH. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature, 1953, 171(4356): 737-738.[10] Chargaff E. Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia, 1950, 6(6): 201-209.[11] Lin HJ, Chargaff E. On the denaturation of deoxyribonu-cleic acid: II. Effects of concentration. Biochim Bio-phys Acta, 1967, 145(2): 398-409.[12] Powdel BR, Satapathy SS, Kumar A, Jha PK, Buragohain AK, Borah M, Ray SK. A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule). DNA Res, 2009, 16(6): 325-343.[13] Wu CI, Maeda N. Inequality in mutation-rates of the two strands of DNA. Nature, 1987, 327(6118): 169-170.[14] Asakawa S, Kumazawa Y, Araki T, Himeno H, Miura KI, Watanabe K. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J Mol Evol, 1991, 32(6): 511-520.[15] Lobry JR. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol, 1996, 13(5): 660-665.[16] Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessières P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Danchin A. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature, 1997, 390(6657): 249-256.[17] Necsulea A, Lobry JR. A new method for assessing the effect of replication on DNA base composition asymmetry. Mol Biol Evol, 2007, 24(10): 2169-2179.[18] Niu DK, Lin K, Zhang DY. Strand compositional asym-metries of nuclear DNA in eukaryotes. J Mol Evol, 2003, 57(3): 325-334.[19] Mugal CF, von Grünberg HH, Peifer M. Transcription-induced mutational strand bias and its effect on sub-stitution rates in human genes. Mol Biol Evol, 2009, 26(1): 131-142.[20] Lobry JR, Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol, 2002, 3(10): RESEARCH0058.[21] Wei W, Guo FB. Strong strand composition bias in the genome of Ehrlichia canis revealed by multiple methods. Open Microbiol J, 2010, 4: 98-102.[22] Tillier ERM, Collins RA. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol, 2000, 50(3): 249-257.[23] Francino MP, Ochman H. Strand asymmetries in DNA evolution. Trends Genet, 1997, 13(6): 240-245.[24] Francino MP, Chao L, Riley MA, Ochman H. Asymmetries generated by transcription-coupled repair in enterobacterial genes. Science, 1996, 272(5258): 107-109.[2 |
