Transcriptomics allows identification of genes and pathways that respond to and counteract biotic and abiotic environmental stresses. The non-targeted nature of transcriptomics allows the identification of novel transcriptional networks in complex systems. For example, comparative analysis of a range of chickpea lines at different developmental stages identified distinct transcriptional profiles associated with drought and salinity stresses, including identifying the role of transcript isoforms of AP2-EREBP. Investigation of gene expression during biofilm formation by the fungal pathogen Candida albicans revealed a co-regulated set of genes critical for biofilm establishment and maintenance.
Transcriptomic profiling also provides crucial information on mechanisms of drug resistance. Analysis of over 1000 isolates of Plasmodium falciparum, a virulent parasite responsible for malaria in humans, identified that upregulation of the unfolded protein response and slower progression through the early stages of the asexual intraerythrocytic developmental cycle were associated with artemisinin resistance in isolates from Southeast Asia.
The use of transcriptomics is also important to investigate responses in the marine environment. In marine ecology, "stress" and "adaptation" have been among the most common research topics, especially related to anthropogenic stress, such as global change and pollution. Most of the studies in this area have been done in animals, although invertebrates have been underrepresented. One issue still is a deficiency in functional genetic studies, which hamper gene annotations, especially for non-model species, and can lead to vague conclusions on the effects of responses studied.