ABSTRACT
We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
Subject(s)
Biological Evolution , Genome, Insect , Wasps/genetics , Animals , Arthropods/parasitology , DNA Methylation , DNA Transposable Elements , Female , Gene Transfer, Horizontal , Genes, Insect , Genetic Speciation , Genetic Variation , Host-Parasite Interactions , Insect Proteins/genetics , Insect Proteins/metabolism , Insect Viruses/genetics , Insecta/genetics , Male , Molecular Sequence Data , Quantitative Trait Loci , Recombination, Genetic , Sequence Analysis, DNA , Wasp Venoms/chemistry , Wasp Venoms/toxicity , Wasps/physiology , Wolbachia/geneticsABSTRACT
The interactions between retroviruses and their hosts can be of a beneficial or detrimental nature. Some endogenous retroviruses are involved in development, while others cause disease. The Genome Parsing Suite (GPS) is a software tool to track and trace all Retroid agents in any sequenced genome (M. A. McClure et al., Genomics 85:512-523, 2005). Using the GPS, the retroviral content was assessed in four model teleost fish. Eleven new species of fish retroviruses are identified and characterized. The reverse transcriptase protein sequences were used to reconstruct a fish retrovirus phylogeny, thereby, significantly expanding the epsilon-retrovirus family. Most of these novel retroviruses encode additional genes, some of which are homologous to cellular genes that would confer viral advantage. Although the fish divergence is much more ancient, retroviruses began infecting fish genomes approximately 4 million years ago.
Subject(s)
Fishes/virology , Retroviridae/genetics , Amino Acid Sequence , Animals , Codon, Terminator , Frameshift Mutation , Genetic Techniques , Genome , Models, Biological , Molecular Sequence Data , Mutation , Phylogeny , RNA-Directed DNA Polymerase , Sequence Homology, Amino Acid , Terminal Repeat SequencesABSTRACT
Retroid agents are genomes that encode the reverse transcriptase (RT) and replicate by way of an RNA intermediate. Some retroid agents are implicated in disease via insertional mutagenesis, while others have been found to encode proteins essential to primate reproduction or provide regulatory sequences for host cell processes. The Genome Parsing Suite (GPS), a generic multistep automated process, was developed to characterize all RT-like sequences in the human genome database and to annotate the gene complement of the retroid agents that encode these sequences. In this report the GPS analyzes all significant WU-tBLASTn hits returned for 30 representative RT queries. A total of 128,779 unique RT signals were identified, and 7594 of these were retrieved by RTs not previously reported in the human genome. We have identified 9652 full-length long interspersed nuclear elements (LINEs). Only 159 LINEs are without stop codons or frameshifts.