title: Patterns of nucleotide asymmetries in plant and animal genomes.
abstract: Symmetry in biology provides many intriguing puzzles to the scientist's mind. Chargaff's second parity rule states a symmetric distribution of oligonucleotides within a single strand of double-stranded DNA. While this rule has been verified in a wide range of microbial genomes, it still awaits explanation. In our study, we inquired into patterns of mono- and trinucleotide intra-strand parity in complex plant genomic sequences that became available during the last few years, and compared these to equally complex animal genomes. The degree and patterns of deviation from Chargaff's second rule were different between plant and animal species. We observed a universal inter-chromosomal homogeneity of mononucleotide skews in coding sequences of plant chromosomes, while the base composition of animal coding sequences differed between chromosomes even within a single species. We also found differences in the base composition of dicot introns in comparison to those of monocots. These genome-wide patterns were limited to genic regions and were not encountered in inter-genic sequences. We discuss the implications of our findings in relation to hypotheses about functional correlations of intra-strand parity which have hitherto been put forward. Furthermore, we propose more recent polyploidization and subsequent homogenization of homoeologues as a possible reason for more homogeneous skew patterns in plants.
authors: Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany. mascher@ipk-gatersleben.de
authors: Martin
authors: M
authors: Mascher
authors: Ingo
authors: I
authors: Schubert
authors: Uwe
authors: U
authors: Scholz
authors: Swetlana
authors: S
authors: Friedel
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics; D002875:Chromosomes / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D016678:Genome / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D008957:Models, Genetic; D009711:Nucleotides / Q000235:genetics*; D012984:Software; D013045:Species Specificity
chemical_list: D009711:Nucleotides