Nucleotide Distribution Patterns in Insect Genomes

This work analyzed genome-wide nucleotide distribution patterns in ten insect genomes. Two internal measures were applied – (i) GC variation and (ii) third codon nucleotide preference. Although the genome size and overall GC level did not show any correlation with insect order, the internal measures usually displayed higher levels of consistency. GC variations in genomes of hymenopteran insects, honeybee and wasp, ranked highest among all eukaryotic genomes analyzed by us. Genomes of honeybee and beetle, insects of different orders with similar overall GC levels, showed significant internal differences. Honeybee genome stood out as unusual due to its high GC variation and 'left-handed' gene locations. Recent sequencing of several insect genomes provides us with an unique opportunity to understand the nature of molecular level evolutionary forces and their manifestation in the phenotypic variations between the organisms [Adams-00, Holt-02, THGSC-06, Xia04, Zdobnov-02]. Much of the earlier genetic knowledge on insects were derived through a narrow prism of analysis of the Drosophila genome, but recent studies on other insects displayed additional unique characteristics. For example, the genome of hymenopteran insect honeybee had much lower GC level than the fly, isochore-like nucleotide distributions and preferences of genes to locate in the AT-rich segments of the genome [Elsik-07, Jorgensen-06, THGSC-06]. Among other insect genomes, GC level in coleopteran insect Tribolium castaneum was as low as honeybee, whereas another hymenopteran insect, Nasonia was GC-rich like Drosophila. These observations prompted us to perform a comparative study of nucleotide distributions in all insect genomes sequenced so far. Here we present the first report of this comparison. With availability of new data, these results will be continually updated at At present, sequencing of ten insect genomes are initiated or completed, and four others are also being considered (Table 1). Their phylogenetic relationship is shown in Fig. 1. All but two of them are from the endpoteran division. Among the endopteran insects, the order Diptera is most well represented with eight members being considered for sequencing. From the other orders such as Hymenoptera, Coleoptera and Lepidoptera, two, one and one representatives are selected respectively. Among ten genomes, where sequencing has been initiated, seven are fully assembled and three are unassembled. Following inferences can be drawn from a comparison of genome sizes and GC levels as shown in Table 1. The genome sizes vary widely from 130Mb in Drosophila to 1384 Mb in Aedes. Incidentally, both limits are represented by insects …