oa Editorial [Hot Topic: Replicating Strand Asymmetry in Bacterial and Eukaryotic Genomes (Guest Editor: Feng-Biao Guo)]

It is my pleasure as a Guest Editor of Current Genomics to present you with a ‘hot topic issue’ on DNA replication. DNA replication adopts a set of asymmetric mechanisms. One of them is the division of leading and lagging strands. In 1991, the nucleotide composition bias between the two replicating strands was originally found in genomes of echinoderm and vertebrate mitochondria. In the following twenty years, more and more bacterial genomes are found to have much different nucleotide composition between the two replicating strands. More importantly, eukaryotes and even mammalians are found to have such strand bias (asymmetry) in recent years. Besides composition bias, there are also other types of biases between two replicating strands, such as gene orientation bias, gene function bias and substitution rate bias. This topic of replicating strand bias has attracted numerous researchers to perform abundant and in-depth researches. In my view, it will continue to be one of the hot topics of genomics. A better understanding of replicating strand asymmetry will greatly advance our knowledge about the mechanism of DNA replication. This theme issue aims mainly to summarize various types of biases between the two replicating strands in bacterial and eukaryotic genomes. Another aim is to try to elucidate the underlying mechanisms of various strand biases. Therefore, this theme issue includes papers reviewing types, extents, application and underlying mechanism of strand asymmetry both in bacterial and eukaryotic genomes. K. Arakawa and M. Tomita reviewed the measures of strand bias that have been proposed to date, including the ΔGC skew, the predictability score of linear discriminant analysis for gene orientation and so on. These methods measure the general composition bias, gene distribution bias and the composition bias of certain oligonucleotides, respectively. Although these measures were predominantly designed for and applied in analyzing replication-related mutational processes of prokaryotes, the authors also give research examples in eukaryotes. X. Xia summarized the diverse patterns of strand asymmetry among different taxonomic groups and made four suggestions. The survey was involved with bacterial, archaeal and mitochondrial genomes. The four suggestions concern the numbers of replication origins and replicating mechanism in certain taxa. Lin et al. reviewed composition bias between light and heavy strands of animal mitochondrial genomes. They discussed the influence of replication-associated mutation pressure on nucleotide and amino acid compositions as well as gene organization in these genomes.....