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The use of transcriptomics is also important to investigate responses in the marine environment<ref name=":0"> {{Cite journal |last=Page |first=Tessa M. |last2=Lawley |first2=Jonathan W. |date=2022 |title=The Next Generation Is Here: A Review of Transcriptomic Approaches in Marine Ecology |url=https://www.frontiersin.org/article/10.3389/fmars.2022.757921 |journal=Frontiers in Marine Science |volume=9 |doi=10.3389/fmars.2022.757921 |issn=2296-7745}}</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" />.
=== Gene function annotation ===
All transcriptomic techniques have been particularly useful in [[Gene annotation|identifying the functions of genes]] and identifying those responsible for particular phenotypes. Transcriptomics of ''Arabidopsis'' [[ecotype]]s that [[Hyperaccumulator|hyperaccumulate metals]] correlated genes involved in [[Bioinorganic chemistry#Metal ion transport and storage|metal uptake]], tolerance, and [[homeostasis]] with the phenotype.<ref name="#19192189">{{cite journal | vauthors = Verbruggen N, Hermans C, Schat H | title = Molecular mechanisms of metal hyperaccumulation in plants | journal = The New Phytologist | volume = 181 | issue = 4 | pages = 759–76 | date = March 2009 | pmid = 19192189 | doi = 10.1111/j.1469-8137.2008.02748.x | url = https://dipot.ulb.ac.be/dspace/bitstream/2013/58126/3/58126.pdf }}</ref> Integration of RNA-Seq datasets across different tissues has been used to improve annotation of gene functions in commercially important organisms (e.g. [[Cucumis sativus|cucumber]])<ref name="#22047402">{{cite journal | vauthors = Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K | title = RNA-Seq improves annotation of protein-coding genes in the cucumber genome | journal = BMC Genomics | volume = 12 | pages = 540 | date = November 2011 | pmid = 22047402 | pmc = 3219749 | doi = 10.1186/1471-2164-12-540 }}</ref> or threatened species (e.g. [[koala]]).<ref name="#25214207">{{cite journal | vauthors = Hobbs M, Pavasovic A, King AG, Prentis PJ, Eldridge MD, Chen Z, Colgan DJ, Polkinghorne A, Wilkins MR, Flanagan C, Gillett A, Hanger J, Johnson RN, Timms P | title = A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity | journal = BMC Genomics | volume = 15 | pages = 786 | date = September 2014 | pmid = 25214207 | pmc = 4247155 | doi = 10.1186/1471-2164-15-786 }}</ref>
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