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Here we identify duplicated genes in five mammalian genomes and classify these duplicates based on the mechanisms by which they were generated. Retrotransposition accounts for at least half of all predicted duplicate genes in these genomes, with tandem and interspersed duplicates comprising the other half. Estimation of the evolutionary rates in each class revealed greater rate asymmetry between retrotransposed...
Gene duplication has long been recognized as a major force in genome evolution and has recently been recognized as an important source of individual variation. For many years the origin of functional gene duplicates was assumed to be whole or partial genome duplication events, but recently retrotransposition has also been shown to contribute new functional protein coding genes and siRNA’s. Here we...
In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony,...
Recent advances in high-throughput sequencing allow researchers to examine the transcriptome in more detail than ever before. Using a method known as high-throughput small RNA-sequencing, we can now profile the expression of small regulatory RNAs such as microRNAs and small interfering RNAs (siRNAs) with a great deal of sensitivity. However, there are many other types of small RNAs (<50nt) present...
Bioinformatic approaches to the identification of genomic sequences having G-quadruplex forming potential (QFP) has enabled important tests of the structure of these sequences in vitro and of their behavior under conditions where the formation or function of G-quadruplexes is modulated in vivo. Several similar approaches to identifying intramolecular QFP (i.e. forming among G-runs on one strand of...
The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]) components of the Drosophila melanogaster and Caenorhabditis...
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