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Transcriptomics allows identification of genes and [[Metabolic pathways|pathways]] that respond to and counteract [[Biotic stress|biotic]] and [[Abiotic stress|abiotic environmental stresses.]]<ref name="#26759178" /><ref name="Govind_2009" /> The non-targeted nature of transcriptomics allows the identification of novel transcriptional networks in complex systems. For example, comparative analysis of a range of [[Cicer arietinum|chickpea]] lines at different developmental stages identified distinct transcriptional profiles associated with [[drought]] and [[salinity]] stresses, including identifying the role of [[Alternative splicing|transcript isoforms]] of [[Apetala 2|AP2]]-[[Ethylene-responsive element binding protein|EREBP]].<ref name="#26759178">{{cite journal | vauthors = Garg R, Shankar R, Thakkar B, Kudapa H, Krishnamurthy L, Mantri N, Varshney RK, Bhatia S, Jain M | title = Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea | journal = Scientific Reports | volume = 6 | pages = 19228 | date = January 2016 | pmid = 26759178 | pmc = 4725360 | doi = 10.1038/srep19228 | bibcode = 2016NatSR...619228G }}</ref> Investigation of gene expression during [[biofilm]] formation by the [[Fungus|fungal]] pathogen ''[[Candida albicans]]'' revealed a co-regulated set of genes critical for biofilm establishment and maintenance.<ref name="#15075282">{{cite journal | vauthors = García-Sánchez S, Aubert S, Iraqui I, Janbon G, Ghigo JM, d'Enfert C | title = Candida albicans biofilms: a developmental state associated with specific and stable gene expression patterns | journal = Eukaryotic Cell | volume = 3 | issue = 2 | pages = 536–45 | date = April 2004 | pmid = 15075282 | pmc = 387656 | doi = 10.1128/EC.3.2.536-545.2004 }}</ref>
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,<ref name="Rich et al">{{cite journal | vauthors = Rich SM, Leendertz FH, Xu G, LeBreton M, Djoko CF, Aminake MN, Takang EE, Diffo JL, Pike BL, Rosenthal BM, Formenty P, Boesch C, Ayala FJ, Wolfe ND | title = The origin of malignant malaria | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 35 | pages = 14902–7 | date = September 2009 | pmid = 19666593 | pmc = 2720412 | doi = 10.1073/pnas.0907740106 | bibcode = 2009PNAS..10614902R | doi-access = free }}</ref> identified that upregulation of the [[unfolded protein response]] and slower progression through the early stages of the asexual intraerythrocytic [[Plasmodium falciparum#
The use of transcriptomics is also important to investigate responses in the marine environment.<ref name=":0"> {{Cite journal |last1=Page |first1=Tessa M. |last2=Lawley |first2=Jonathan W. |date=2022 |title=The Next Generation Is Here: A Review of Transcriptomic Approaches in Marine Ecology |journal=Frontiers in Marine Science |volume=9 |doi=10.3389/fmars.2022.757921 |issn=2296-7745|doi-access=free }}</ref> In marine ecology, "[[Stress (biology)|stress]]" and "[[adaptation]]" have been among the most common research topics, especially related to anthropogenic stress, such as [[global change]] and [[pollution]].<ref name=":0" /> Most of the studies in this area have been done in [[Animal|animals]], although [[Invertebrate|invertebrates]] have been underrepresented.<ref name=":0" /> One issue still is a deficiency in functional genetic studies, which hamper [[Gene annotation|gene annotations]], especially for non-model species, and can lead to vague conclusions on the effects of responses studied.<ref name=":0" />
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