Two common profiles exist for genomic oligonucleotide frequencies

BMC Research Notes

Lei Wang¹  Shang-Hong Zhang¹ 

[1] Key Laboratory of Gene Engineering of Ministry of Education, and Biotechnology Research Center, Sun Yat-sen University, Guangzhou, 510275, China

关键词: Strand symmetry;    GC content;    Frequency profile;    Oligonucleotide;    Genomic sequence;   

Others  :  1165197
DOI  :  10.1186/1756-0500-5-639

 received in 2012-01-24, accepted in 2012-11-14,  发布年份 2012

【 摘 要 】

Background

It was reported that there is a majority profile for trinucleotide frequencies among genomes. And further study has revealed that two common profiles, rather than one majority profile, exist for genomic trinucleotide frequencies. However, the origins of the common/majority profile remain elusive. Moreover, it is not clear whether the features of common profile may be extended to oligonucleotides other than trinucleotides.

Findings

We analyzed 571 prokaryotic genomes (chromosomes) and some selected eukaryotic nuclear genomes as well as other genetic systems to study their compositional features. We found that there are also two common profiles for genomic oligonucleotide frequencies: one is from low-GC content genomes, and the other is from high-GC content genomes. Furthermore, each common profile is highly correlated to the average profile of random sequences with corresponding GC content and generated according to first-order symmetry.

Conclusions

The causes for the existence of two common profiles would mainly be GC content variations and strand symmetry of genomic sequences. Therefore, both GC content and strand symmetry would play important roles in genome evolution.

【 授权许可】

   
2012 Zhang and Wang; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Bernardi G: The compositional evolution of vertebrate genomes. Gene 2000, 259:31-43.
• [2]Lobry JR, Sueoka N: Asymmetric directional mutation pressures in bacteria. Genome Biol 2002, 3:Research0058.1-0058.14. BioMed Central Full Text
• [3]Mann S, Chen Y-PP: Bacterial genomic G+C composition-eliciting environmental adaptation. Genomics 2010, 95:7-15.
• [4]Forsdyke DR, Mortimer JR: Chargaff’s legacy. Gene 2000, 261:127-137.
• [5]Baisnée PF, Hampson S, Baldi P: Why are complementary DNA strands symmetric? Bioinformatics 2002, 18:1021-1033.
• [6]Albrecht-Buehler G: Asymptotically increasing compliance of genomes with Chargaff’s second parity rules through inversions and inverted transpositions. Proc Natl Acad Sci USA 2006, 103:17828-17833.
• [7]Zhang S-H, Huang Y-Z: Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA. Bioinformatics 2010, 26:478-485.
• [8]Karlin S, Burge C: Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 1995, 11:283-290.
• [9]Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B: Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol 1999, 16:1391-1399.
• [10]Zhang S-H, Huang Y-Z: Characteristics of oligonucleotide frequencies across genomes: conservation versus variation, strand symmetry, and evolutionary implications. Nature Precedings 2008. http://hdl.handle.net/10101/npre.2008.2146.1 webcite (last accessed date June 16, 2012)
• [11]Albrecht-Buehler G: The three classes of triplet profiles of natural genomes. Genomics 2007, 89:596-601.
• [12]Zhang S-H, Wang L: A novel common triplet profile for GC-rich prokaryotic genomes. Genomics 2011, 97:330-331.
• [13]Albrecht-Buehler G: Inversions and inverted transpositions as the basis for an almost universal “format” of genome sequences. Genomics 2007, 90:297-305.
• [14]Pačes J, Zíka R, Pačes V, Pavlíček A, Clay O, Bernardi G: Representing GC variation along eukaryotic chromosomes. Gene 2004, 333:135-141.
• [15]Costantini M, Clay O, Auletta F, Bernardi G: An isochore map of human chromosomes. Genome Res 2006, 16:536-541.
• [16]Mitchell D, Bridge R: A test of Chargaff’s second rule. Biochem Biophys Res Commun 2006, 340:90-94.
• [17]Nikolaou C, Almirantis Y: Deviations from Chargaff’s second parity rule in organellar DNA: insights into the evolution of organellar genomes. Gene 2006, 381:34-41.