MiR-133b or ctrl miR was transfected either alone or together with ctrl or specific amiR-133b

Metazoan for non-regulated genes and 55.9% Metazoan for repressed genes. This difference in proportion Metazoan is highly significant; induced genes are also much more likely to be wasp-specific. A potential confounding factor, however, is gene length, as it is more difficult to detect homology among short genes. Rapidly diverging short genes, even when they are evolutionarily orthologous to genes in other species, may be nearly impossible to classify as such. We use two approaches to control for gene length. First, we consider only genes encoding proteins with sizes in the interquartile range of the induced class. Even restricting our analysis to genes encoding these small proteins, induced genes remain much younger than The Infection-Induced Transcriptome of Nasonia other classes. In this restricted set, induced genes are also more likely to be waspspecific. As a second approach, we fit a logistic regression using an indicator variable set to 0 if gene age is “Metazoa” as the response variable, and using gene size and an indicator variable set to 1 if differential expression class is induced as predictor variables. As expected, size is significantly negatively associated with gene youth, with larger genes less likely to be classified as young. Notably, being induced is positively associated with gene youth, even when including size as a cofactor in the model. We get identical results if we define “gene youth”as being wasp-specific, instead of as not being present in the common ancestor of Metazoans. Both these lines of evidence suggest that induced genes are significantly younger than non-regulated, and repressed genes, and specifically that induced genes are more likely to be taxonomically-restricted to a subset of lineages within Metazoans. UPF 1069 supplier Discussion The number of sequenced insect genomes is likely to grow dramatically in the next few years, as the i5K project and related efforts begin to bear fruit. The challenge now is to make biological sense of the genomic data being produced. Taxonomicallyrestricted genes, especially those that seem to have arisen de novo from non-coding sequence, are likely more crucial to organismal fitness than previously recognized, and it is becoming clear that 8014858 these genes may be a common feature of many genomes. In light of this, homology-based methods of functional gene annotation will be suitable for only a subset of the genome. While functional 15126366 analysis of single genes and pathways will always have an important role to play in understanding the biology of diverse insects, such techniques are not scalable to multiple genomes across many species. RNA-seq technology offers a rapid and scalable approach to characterize how gene expression changes in response to experimental manipulations, and is applicable across a wide range of taxa. The innate immune system is particularly amenable to characterization with expression-based methodology such as RNA-seq, as one of the key biological consequences of pathogenic infections is the rapid induction of several classes of effector proteins, along with up-regulation of a number of other pathway components. This process has been extremely well-studied in D. melanogaster, but historically has been challenging to study in other insects where molecular tools to measure gene expression have not been as well developed. In this study, we have characterized the immune-inducible transcriptome in N. vitripennis using RNA-sequencing, and identified genes that respond transcri