| With the advent of sequencing technology, nuclear genomes of about 20 insect species and mitochondrial genomes of about 100 insect species have been acquired. In order to unveil the hidden biological and evolutionary information, it is not enough to acquire only genome sequence, deep analysis of known genome is needed. Nowadays, there are increasing data in the database, the corresponding analysis tools are also increasing, which provide great convenience for biology researchers.Insect (Insect, Hexapod, Arthropod) is the largest group in the earth. The studies of entomology are important for maintaining ecological balance of the earth, promoting sustainable development, controlling insect pests in agriculture and forestry. There are two genomes in insects, nuclear genome and mitochondrial genome. There are many non-coding regions, repeat sequences, introns and recombination regions in the nuclear genomes, which are different among species; the composition of mitochondrial genomes are usually conservative in the same phylum, which exist as closed circular strands with 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. Furthermore, Wolbachia as an intracellular bacterium could infect most insect. They are gram-negative alpha-proteobacteria, and they could infect a range of arthropods and filarial nematodes. Wolbachia can alter host biology by reproductive manipulation in several means such as induction of thelytokous parthenogenesis, ferminization of genetic males, male killing, and egg-sperm incompatibility. Our studies make use of bioinformatics methods, such as Corresponding Analysis, Chi-square Test, and Likelihood Ratio Test and so on, to detect codon usage bias, trend of codon usage evolution and the relationship between nuclear genome, mitochondrial genome and Wolbachia genome.The proteins coded by mitochondrial genomes are important for maintaining life of organism. This study analyzed the relationship between codon usage and tRNA abundance in insect mitochondrial genomes. The results showed that there were 10 of 22 optimal codons could not pair with anticodons. This finding is inconsistent with previous studies in mammal, fish and fungal. So it is inferred that codon usages are not influenced by tRNA abundance in insect mitochondrial genomes, and both codon usages and anticodons evolve independently. Non-optimal codon-anticodon usages are common in insect mitochondrial genomes, and the mechanism is needed to be further studied.The proteins coded by mitochondrial genomes can not work by themselves, and they require the proteins that are coded by nuclear genes to make up of the multi-protein complexes of Electron Transfer Chain (ETC), in order to produce energy, and this process is called Oxidative phosphorylation (OXPHOS). OXPHOS process is the only process under control of both nuclear and mitochondrial genomes, they coevolve with each other. This study take Drosophila melanogaster as an example to investigate the differences in codon usages in the genes coevolved in the OXPHOS system. Results showed that codon usages of nuclear genes involved in the OXPHOS system of D. melanogaster primarily experienced translational selection and nucleotide composition. Using Corresponding Analysis (COA), no specific factor could be identified as affecting codon usage in mitochondrial genes, which maybe subject to its origin, not constrained by function. Although nuclear genes and mitochondrial genes have relative function and coevolve with each other, they have different codon usage patterns, coadaptation may occur through selection on tertiary structure. Codon usages in both genomes are affected by context-dependent mutations.There might be also another important genome except for nuclear genome and mitochondrial genome in insect cells, Wolbachia genome. Because the genome of Wolbachia is similar to the mitochondrial genome of animals, such as the common ancestor alpha-proteobacteria, maternally inherited, whether the evidences of common origin could be found in the aspect of codon usage or genome composition in both Wolbachia nuclear genome and insect mitochondrial genome or not? This study took Wolbachia pipientis wMel as example, results showed that AT content was very high in Wolbachia pipientis wMel genome, and AT-rich codons were selected regardless of high expression level or low expression level. An Nc-plot showed that the genome may suffer from a nucleotide composition bias. Analysis of COA suggested that gene length (R = 0.123, P < 0.01) and gene expression level (R = -0.312, P < 0.01) also played an important role in shaping codon usage bias. As gram-negative alpha-proteobacteria, the genome of Wolbachia is similar to animal mitochondrial genome, such as high AT content, which confirmed the relationship between Wolbachia genome and mtDNA again.In the above analyses, we used an important parameter: Codon Adaptation Index (CAI). Although there is a little dispute with this parameter, it is great useful. It will spend more time and money in detecting the expression level of genes within the genomes available so far, and then the CAI values can be used to estimate the expression level of unknown genes. CAI is a single value measurement that summarizes the codon usage of a gene relative to the codon usage of a reference set of genes. CAI value is between 0 and 1.0, and the higher values mean the higher expression level. In present, there are 10 Drosophila complete genomes that have been sequenced, which provide enough data for biology research. In this study, CYP6A20 genes that related to aggressive were downloaded from 7 Drosophila species and CAI value of CYP6A20 genes were compared to infer the aggressive level of these 7 Drosophila species. It was a pity that the results of CAI value maybe irresponsible, but CAI values would be used more and more in the post genomic era.Selection analysis based on codon usage level is important for studying gene evolution. This study would detect adaptive evolution on cytochrome c oxidase subunit I in insect mitochondrial genomes. Insect are the largest community in the earth, although the mitochondrial genomes in the phylum are conservative, the mtDNA have obvious differences in sequences. With the advent of post-genome era, there are more and more mitochondrial genomes in the databases, which provide a chance for us to gain new insight into the evolution of COI genes across insect species. The results indicated that the COI genes would suffer from strong purifying selection through the analysis of 31 COI genes of insect mitochondrial genomes. But the survive pressure varied obviously from one to another, the COI genes must evolve to adapted to the environment pressure. Selection analysis was conducted by codeml program PAML 4.0, and 12 positive sites were detected only in the comparison of Model 7 & Model 8. The positive selection of 395 sites was significance, whereas the positive selections of other 11 sites were not significance. This result was consistent with the evolutionary characters of mitochondrial genome, which validated the conservation of mitochondrial genes.
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