Alternative splicing increases the transcriptome diversity in eukaryotes. In insects, alternative splicing may causes resistance to pesticides and Bt toxins. The alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) has not been studied. To investigate its alternative splicing pattern and relation to Bt resistance, we carried out single-molecule real-time (SMRT) transcript sequencing and Iso-seq analysis on resistant, eCry3.1Ab-selected and susceptible, unselected, western corn rootworm neonate midguts which fed on seedling maize with and without eCry3.1Ab for 12 and 24 hours. We present transcriptome-wide alternative splicing patterns of western corn rootworm midgut in response to feeding on eCry3.1Ab-expressing corn using a comprehensive approach that combines both RNA-seq and SMRT transcript sequencing techniques. We found that 67.73% of multi-exon genes are alternatively spliced, which is consistent with the high transposable element content of the genome. One of the alternative splicing events we identified was a novel peritrophic matrix protein with two alternative splicing isoforms. Analysis of differential exon usage between resistant and susceptible colonies showed that in eCry3.1Ab-resistant western corn rootworm, expression of one isoform was significantly higher than in the susceptible colony, while no significant differences between colonies were observed with the other isoform. Our results provide the first survey of alternative splicing in western corn rootworm and suggest that the observed alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.

中文翻译：

---

使用RNA-seq和PacBio Iso-Seq检测与Bt抗性相关的西方玉米根虫（Diabrotica virgifera virgifera LeConte）的可变剪接

选择性剪接增加了真核生物的转录组多样性。在昆虫中，选择性剪接可能导致对农药和Bt毒素的抵抗。尚未研究西部玉米根虫（Diabrotica virgifera virgifera LeConte）中的替代剪接。为了研究其替代剪接模式以及与Bt抗性的关系，我们对抗性，经eCry3.1Ab选择和易感，未经选择的西部玉米根虫新生中肠进行了单分子实时（SMRT）转录本测序和Is-seq分析。在有和没有eCry3.1Ab的玉米上饲喂12和24小时。我们提出了西部玉米根虫中肠的转录组范围的可变剪接模式，以响应以eCry3为食。使用结合RNA-seq和SMRT转录测序技术的综合方法表达1Ab的玉米。我们发现67.73％的多外显子基因被交替剪接，这与基因组的高转座因子含量一致。我们确定的替代剪接事件之一是具有两个替代剪接同工型的新型营养缺陷型基质蛋白。抗性和易感菌落之间差异外显子使用的分析表明，在耐eCry3.1Ab的西部玉米根虫中，一种同工型的表达显着高于易感菌落，而在另一种同工型之间未观察到显着差异。