Gossypium hirsutum sequencing after Helicoverpa armigera and Aploygus lucorum feeding

The green mirid bugs (Apoygus lucorum) and the cotton bollworms (Helicoverpa armigera) are both preferred to living on cotton and cause different symptoms suggesting specialized responses in cotton to the two insects. We performed depth analysis of cotton transcriptomes at both transcription and splicing levels to have deep insights into cotton plant defenses against A. lucorum and H. armigera. At the transcription level, Jasmonate (JA) signaling might have more contribution than salicylic acid (SA) signaling in defense against H. armigera whereas SA might be more dominating in defense against A.lucorum. The transcriptions of some PRs were induced by both insects and the inductions are obviously higher by A.lucorum indicating more important roles of PRs in the defense against A. lucorum. From the five clades of serine protease inhibitors (SPIs) genes, the clade 1 exhibited higher induction by H. armigera whereas clade 3 and part of the clade 4 were more highly induced by A.lucorum. We further identified one SPI in clade 1 with insecticide functions on H. armigera. Insect feedings also had obvious impacts on the gene alternative splicing (AS) events. Most AS events are occurred on the genes which have no obvious change in transcription level. The differential AS events caused by H. armigera are largely different from that by A.lucorum. Together, our study demonstrated that the cotton defense response to insects are distinguished at both the gene transcription and alternative splicing levels.