Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat

Wheat (Triticum aestivum L.), a globally important crop, is challenged by increasing temperatures (heat stress, HS). However its polyploid nature, the incompleteness of its genome sequences and annotation, the lack of comprehensive HS-responsive transcriptomes and the unexplored heat sensing and signaling of wheat hinder our full understanding of its adaptations to HS. The recently released genome sequences of wheat, as well as emerging single-molecular sequencing technologies, provide an opportunity to thoroughly investigate the molecular mechanisms of the wheat response to HS. We generated a high-resolution spatio-temporal transcriptome map of wheat flag leaves and filling grain under HS at 0 min, 5 min, 10 min, 30 min, 1 h and 4 h by combining full-length single-molecular sequencing and Illumina short reads sequencing. This hybrid sequencing newly discovered 4947 loci and 70 285 transcripts, generating the comprehensive and dynamic list of HS-responsive full-length transcripts and complementing the recently released wheat reference genome. Large-scale analysis revealed a global landscape of heat adaptations, uncovering unexpected rapid heat sensing and signaling, significant changes of more than half of HS-responsive genes within 30 min, heat shock factor-dependent and -independent heat signaling, and metabolic alterations in early HS-responses. Integrated analysis also demonstrated the differential responses and partitioned functions between organs and subgenomes, and suggested a differential pattern of transcriptional and alternative splicing regulation in the HS response. This study provided comprehensive data for dissecting molecular mechanisms of early HS responses in wheat and highlighted the genomic plasticity and evolutionary divergence of polyploidy wheat.