Alternative transcriptomes and plant resilience: technological innovations and biological insights

The development of advanced high-throughput sequencing approaches has revealed the biomolecular diversity associated with central genetic dogmas like never before. Big genomics data highlight the hidden complexity of the genetic regulation of cellular machinery and physiological responses to environmental stimuli. The investigation and identification of alternative mRNA forms and protein diversity as adaptation mechanisms to environmental stimuli is one such case of unparallel genetic complexity in plant cells. Alternative splicing and selection of alternative start and stop sites during and after transcription lead to conditional variants across protein families. The biological importance of many such proteins is well understood, especially during reprogramming of plant stress responses and development. Interestingly, valuable methodologies and technical leads in the genome and alternative transcriptome sequencing from animals and model plants are now laying the groundwork for similar studies in crops. However, identifying alternative transcriptomes remains a major challenge for higher plants. Therefore, there is a need for improved library preparation methods and data analysis pipelines. We sought to examine the status of alternative transcriptome-associated studies on plant physiological regulation in response to environmental adaptation. In addition, we evaluated the recent technological advances available for studying alternative transcriptomes in plants.