Identification and comparison of key RNA interference machinery from western corn rootworm, fall armyworm, and southern green stink bug.

RNA interference (RNAi)-based technology shows great potential for use in agriculture, particularly for management of costly insect pests. In the decade since the insecticidal effects of environmentally-introduced RNA were first reported, this treatment has been applied to several types of insect pests. Through the course of those efforts, it has become apparent that different insects exhibit a range of sensitivity to environmentally-introduced RNAs. The variation in responses across insect is not well-understood, with differences in the underlying RNAi mechanisms being one explanation. This study evaluates eight proteins among three agricultural pests whose responses to environmental RNAi are known to differ: western corn rootworm (Diabrotica virgifera virgifera), fall armyworm (Spodoptera frugiperda), and southern green stink bug (Nezara viridula). These proteins have been identified in various organisms as centrally involved in facilitating the microRNA- and small interfering-RNA-mediated interference responses. Various bioinformatics tools, as well as gene expression profiling, were used to identify and evaluate putative homologues for characteristics that may contribute to the differing responses of these insects, such as the absence of critical functional domains within expressed sequences, the absence of entire gene sequences, or unusually low or undetectable expression of critical genes. Though many similarities were observed, the number of isoforms and expression levels of double-stranded RNA-binding and argonaute proteins varied across insect. Differences among key RNAi machinery genes of these three pests may impact the function of their RNAi pathways, and therefore, their respective responses to exogenous RNAs.

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize.

Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.