Hello Ayat

Yes, it is possible. If your plant sample is infected with an RNA virus or even a viroid, you may have a portion of reads which does not map to your plant ref seq. Then you may find the species of the contaminant source by BLASTing those unmapped reads against databases to find what is the possible source of foreign RNA sequences.

Regards

Yes, it is possible.

I believe these papers have the methods as how you identify these sequences

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116224/

https://nanoporetech.com/resource-centre/wheat-virus-identification-within-infected-tissue-using-nanopore-sequencing

Is there reference genome for your species! If so, would be easy. Just take unmapped reads to make de novo assembly by using RNA-Seq assembler like Trinity, then annotate contigs by blast. If there is no reference genome, you will have to work harder! You should annotate whole transcriptome assembly against serevel databases!

Regrads,

Yes, it is possible with Dual RNA-Seq technique. This technique allow us to apply RNA sequencing of two species at the same time. Thus it is possible to directly study the gene expression of two interacting species without the need to physically separate cells or RNA.

There is a link for an amazing review paper which can be useful:

Article Two's company: studying interspecies relationships with dual RNA-seq

Also there many researches using this method like:

https://academic.oup.com/jhered/article/107/2/163/2622859

Article Large-Scale Transcriptome Analysis of Cucumber and Botrytis ...

Article RNA CoMPASS: a dual approach for pathogen and host transcrip...

https://mbio.asm.org/content/6/6/e01765-15.short

https://www.nature.com/articles/nprot.2016.090

Regards

Hi there, my answer may be simple, but before starting in long blast search if I were you I would use software such as Kraken on your reads. This software will return classify all the reads according to the Taxon ID they come from. In this way you can have an idea of how many reads you have that come from a different organism and which this organism is. You can then parse the corresponding reads and, if you have enough, even attempt a de novo assembly.

If it's viruses what you are looking for, then you can downloaded the virus genome database from NCBI and align your reads on it using a read aligner such as bwa or bowtie2. Looking at the coverage of the sequences you can have an idea of the presence of each specific virus. I personally used this approach to discover Grapevine mosaic virus from a RNA-seq sample of vitis vinifera

Thank you all for your advantageous guidelines. Ali Javadmanesh , Hatem Zayed , Aboozar Soorni , Mehdi Soltani Howyzeh , Salvatore Camiolo

Most welcome