Dr Tyagi

off course you  can use the ITS primer for the detection of fungus. Plenty of literatures are available for the same.

Make sure the RT-PCR is not amplifying contaminating genomic DNA.  I like to include an intron (~50 bp in fungi) between primer sites, so I can distinguish between amplicons from cDNA and gDNA on a gel.

Also, it is often best to used a single-copy, 'constitutive', coding gene as your house keeping gene, if you're using it to normalize expression of another single-copy coding gene.  If you're not unsure (see other RT-PCR papers using the same fungus) try several house keeping genes (e.g. EF1a, actin, a ribosomal protein) and analyze separately.  There are many RNASeq analyses articles now that identify the most stable house keeping genes in several species.

I'm not sure about using RT-PCR as a viability measure.  You should compare it to established tests: e.g. CFU dilutions and staining with vital dyes (esp. using flow cytometry w single cell fungi).

Hello Swati

Some references 1

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQFggpMAE&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4059633%2F&usg=AOvVaw0EmfeDWpOmu9071dz8ne5S

2

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQFggyMAI&url=http%3A%2F%2Faem.asm.org%2Fcontent%2F79%2F8%2F2519.full&usg=AOvVaw2YOpSWIpXIcXHGfJyir0HA

3

https://books.google.iq/books?id=e3HQ237OWy4C&pg=PA561&lpg=PA561&dq=ITS+region+fungi,+endogenous+RT-PCR&source=bl&ots=Bb30cfk9K9&sig=Rh9AeBEjaZHLSdg7DLaZYEOaVxg&hl=en&sa=X&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQ6AEISzAJ

4

https://books.google.iq/books?id=4Kg-DwAAQBAJ&pg=PA164&lpg=PA164&dq=ITS+region+fungi,+endogenous+RT-PCR&source=bl&ots=V7LGkwrLV6&sig=hT4-JrkcPW7MvM6aJJwYYFpuVoM&hl=en&sa=X&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQ6AEITTAK

5

https://books.google.iq/books?id=Tr9joZRnZIsC&pg=PA86&lpg=PA86&dq=ITS+region+fungi,+endogenous+RT-PCR&source=bl&ots=ujRYefGlhR&sig=jFpWtRPsufTneckNW1TaVFc6BAk&hl=en&sa=X&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQ6AEITzAL

6

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=13&cad=rja&uact=8&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQFghRMAw&url=http%3A%2F%2Fjcm.asm.org%2Fcontent%2F40%2F8%2F2860.long&usg=AOvVaw0d2foN2hadutFMsQbDYQXJ

7

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=14&cad=rja&uact=8&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQFghWMA0&url=http%3A%2F%2Fwww.scielo.br%2Fscielo.php%3Fscript%3Dsci_arttext%26pid%3DS1516-89132013000100019&usg=AOvVaw21YnawoUvhYltFwaITspMu

8

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=15&cad=rja&uact=8&ved=0ahUKEwiWtLKtl97YAhVKiywKHezXAhQQFghfMA4&url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FInternal_transcribed_spacer&usg=AOvVaw1zGO18tWUGae7h5qrKspb9

9

https://www.sciencedirect.com/science/article/pii/S1198743X14631001

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=12&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCCswAQ&url=https%3A%2F%2Fwww.thermofisher.com%2Fza%2Fen%2Fhome%2Flife-science%2Fpcr%2Freal-time-pcr%2Freal-time-pcr-assays.html&usg=AOvVaw31vR7Iubr08gbuYqbmF8zU

11

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=13&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCDAwAg&url=http%3A%2F%2Fpubs.acs.org%2Fdoi%2Fabs%2F10.1021%2Fjf102092c&usg=AOvVaw3Eam6irIoTcF1MZBqvETE7

12

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=14&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCDowAw&url=http%3A%2F%2Fwww.tandfonline.com%2Fdoi%2Fpdf%2F10.1080%2F17429145.2017.1397205&usg=AOvVaw2HyUePRadKR1F9r9Nol3Ap

13

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=15&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCD0wBA&url=http%3A%2F%2Fwww.plantcell.org%2Fcontent%2F12%2F7%2F1165.full.pdf&usg=AOvVaw3zLiqlpqAvWfB7wvx5jMeV

14

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=16&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCEIwBQ&url=https%3A%2F%2Fstud.epsilon.slu.se%2F4709%2F21%2Fassefa_jima_t_120918.pdf&usg=AOvVaw0Y-B4asgKoL44vHjSELPNx

15

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=17&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCEswBg&url=http%3A%2F%2Fwww.ijo.in%2Farticle.asp%3Fissn%3D0301-4738%3Byear%3D2007%3Bvolume%3D55%3Bissue%3D4%3Bspage%3D261%3Bepage%3D266%3Baulast%3DBagyalakshmi&usg=AOvVaw1qPlYsS6Nzi-yjevTQtKtM

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=18&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCFMwBw&url=https%3A%2F%2Flink.springer.com%2Fcontent%2Fpdf%2F10.1186%2F1741-7007-7-88.pdf&usg=AOvVaw0r1jH6GkJkkqM7MkeU_Pjy

17

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=19&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCFkwCA&url=http%3A%2F%2Fgenesdev.cshlp.org%2Fcontent%2F16%2F20%2F2662.full&usg=AOvVaw1gZutDTMb2rl8qIXFeWCz_

18

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=20&cad=rja&uact=8&ved=0ahUKEwj4_rzamN7YAhXMhKYKHUsLCg84ChAWCGEwCQ&url=http%3A%2F%2Fwww.dfo-mpo.gc.ca%2Fscience%2Faah-saa%2Fdiseases-maladies%2Fcpfdcy-eng.html&usg=AOvVaw2S6wlUKvUkWn4OF1Qktnsx

19

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=21&cad=rja&uact=8&ved=0ahUKEwiNgM2Ym97YAhXGPhQKHZcPCVU4FBAWCCYwAA&url=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs10658-011-9920-1&usg=AOvVaw0VO6FWPg_mas1IIf32zcY6

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=23&cad=rja&uact=8&ved=0ahUKEwiNgM2Ym97YAhXGPhQKHZcPCVU4FBAWCDQwAg&url=http%3A%2F%2Fwww.ijo.in%2Farticle.asp%3Fissn%3D0301-4738%3Byear%3D2007%3Bvolume%3D55%3Bissue%3D4%3Bspage%3D261%3Bepage%3D266%3Baulast%3DBagyalakshmi&usg=AOvVaw1qPlYsS6Nzi-yjevTQtKtM

Thank you everyone for your valuable suggestions

Why not.

Sure U can!

I echo what Marek, Al Ani & S MuralI said.

Try several times & be sure of no contaminants.