Differential Transcription and Alternative Splicing in Cotton Underly Specialized Defense Responses Against Pests

The green mirid bug (Apolygus lucorum) and the cotton bollworm (Helicoverpa armigera) are both preferred to live on cotton but cause different symptoms, suggesting specialized responses of cotton to the two insects. In this study, we investigated differential molecular mechanisms underlying cotton plant defenses againstA. lucorumandH. armigera viatranscriptomic analyses. At the transcription level, jasmonate (JA) signaling was dominated in defense againstH. armigerawhereas salicylic acid (SA) signaling was more significant in defense againstA. lucorum. A set of pathogenesis-related (PR) genes and protease inhibitor genes were differentially induced by the two insects. Insect infestations also had an impact on alternative splicing (AS), which was altered more significantly by theH. armigerathanA. lucorum. Interestingly, most differential AS (DAS) genes had no obvious change at the transcription level. GO analysis revealed that biological process termed RNA splicing and cellular response to abiotic stimulus were enriched only in DAS genes from theH. armigerainfested samples. Furthermore, insect infestations induced the retained intron of GhJAZs transcripts, which produced a truncated protein lacking the intact Jas motif. Taken together, our data demonstrate that the specialized cotton response to different insects is regulated by gene transcription and AS as well.