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=== Mycological barcoding ===
{{Main|Fungal DNA barcoding}}
The ITS region is the most widely sequenced DNA region in [[molecular ecology]] of [[fungi]]<ref>{{cite journal |author1=Peay K.G. |author2=Kennedy P.G. |author3=Bruns T.D. | title=Fungal community ecology: a hybrid beast with a molecular master| journal=BioScience| year=2008 |pages=799–810|volume=58|issue=9 | doi=10.1641/b580907|s2cid=18363490 |doi-access=free }}</ref> and has been recommended as the universal fungal [[DNA barcoding|barcode]] sequence.<ref>{{cite journal | author=Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W., Bolchacova, E., Voigt, K., Crous, P.W. | title=Nuclear Ribosomal Internal Transcribed Spacer (ITS) Region as a Universal DNA Barcode Marker for Fungi | journal=PNAS| year=2012 |doi= 10.1073/pnas.1117018109| pages=6241–6246|volume=109 | issue=16|display-authors=etal | pmid=22454494 | pmc=3341068| doi-access=free }}</ref> It has typically been most useful for molecular systematics at the species to genus level, and even within species (e.g., to identify geographic races). Because of its higher degree of variation than other genic regions of rDNA (for example, small- and large-subunit rRNA), variation among individual rDNA repeats can sometimes be observed within both the ITS and IGS regions. In addition to the universal ITS1+ITS4 primers<ref>White, T.J., Bruns, T., Lee, S., and Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: a Guide to Methods and Applications 18, 315–322.</ref><ref>The ITS1 primer covers ITS1-5.8S-ITS2 from the 5', and ITS4 covers the same area from the 3'.</ref> used by many labs, several taxon-specific primers have been described that allow selective amplification of fungal sequences (e.g., see Gardes & Bruns 1993 paper describing amplification of [[basidiomycete]] ITS sequences from [[mycorrhiza]] samples).<ref>{{cite journal |author1=Gardes, M. |author2=Bruns, T.D.| title=ITS primers with enhanced specificity for basidiomycetes: application to the identification of mycorrhiza and rusts| journal=Molecular Ecology| year=1993 |doi= 10.1111/j.1365-294X.1993.tb00005.x| pages=113–118|volume=2|pmid=8180733 | issue=2|s2cid=24316407}}</ref> Despite [[shotgun sequencing]] methods becoming increasingly utilized in microbial sequencing, the low biomass of fungi in clinical samples make the ITS region amplification an area of ongoing research.<ref>{{Cite journal|last1=Usyk|first1=Mykhaylo|last2=Zolnik|first2=Christine P.|last3=Patel|first3=Hitesh|last4=Levi|first4=Michael H.|last5=Burk|first5=Robert D.|date=2017-12-13|editor-last=Mitchell|editor-first=Aaron P.|title=Novel ITS1 Fungal Primers for Characterization of the Mycobiome|journal=mSphere|volume=2|issue=6|pages=e00488–17, /msphere/2/6/mSphere0488–17.atom|doi=10.1128/mSphere.00488-17|issn=2379-5042|pmc=5729218|pmid=29242834}}</ref><ref>{{Cite journal|last1=Nilsson|first1=R. Henrik|last2=Anslan|first2=Sten|last3=Bahram|first3=Mohammad|last4=Wurzbacher|first4=Christian|last5=Baldrian|first5=Petr|last6=Tedersoo|first6=Leho|date=February 2019|title=Mycobiome diversity: high-throughput sequencing and identification of fungi|journal=Nature Reviews Microbiology|volume=17|issue=2|pages=95–109|doi=10.1038/s41579-018-0116-y|pmid=30442909|s2cid=53438777|issn=1740-1534}}</ref>