I am currently doing the NGS data analysis of miRNAs from my plant samples and after pre processing the reads were aligned against plant miRNAs from miRBase. In the proceeding step all paper references showed the reads were mapped to a reference genome or ESTs for miRNA prediction, but the whole genome of our plant has not sequenced and no ESTs are available. Could any one please help me regarding this?
Hello,
I am not a specialist but I think you can try a miRNA sequencing. Make an RNA extraction and separe small RNA (some kit can do it in few steps). Prepare your sample depending on the sequencing method you can use. Then sequence. Repeat the operation several time.
Use a computationnal approach like this one "miReader: Discovering Novel miRNAs in Species without Sequenced Genome" (plos one)
Have a good day
Since you do not have the reference genome, the small RNA data after adapter removal can be blasted both with the mature miRNA and hairpins from miRBase. This will give you information on the conserved and known miRNA. For the prediction of novel miRNA, the data which does not show any hit in miRBase, can be aligned onto the closest reference genome, and then prediction can be done using mireap software. Hope this will help.
hi, we have done that for an eucaliptus species using predictions made from A. thaliana and crossing it with small-rna-seq data
Thanks Yi Xu. we don't even have the transcriptome data of our plant samples.
Thanks Andreia
Hello Nadiya. The data from transcriptome of plants near your plant, either in genus or family can be very useful.
Hi Zaida, thank you. We are planning to proceed with the closest reference genome and miReader. We are also proceeding the transcriptome sequencing of our plant.
Hello Nadiya. I agree with Zaida. A first approach is to use data from the closest transcriptome to your plant.
Hi Everyone,
I am new to NGS and performing somewhat similar analysis; Though in my case I do have some EST fasta sequences present for my organism
I have already done iterative mapping of my samples using the EST sequences as my reference genome
Which tool can I use for further analysis?
I want to find out known microRNA families, known miRNA variants, small RNA length, novel miRNAs, targets of novel miRNAs, structure of precursors of novel miRNA, GO ontology, KEGG pathway...
Any suggestions are welcome
Hi Prenali Sonpatki,
Our case is a plant sample. The known as well conserved miRNAs can be identified from miRBase (Using Bowtie). We have predicted novel miRNAs with mirDeep tool.. Best option for plant miRNA target prediction is psRNA target. Then proceed to annotation with AGRI go tool.
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