We had generated mitochondrial genome of frog using Ion Torrent PGM platform. The genome is missing two tRNAs namely t-His and t-Ser. what could be the reason for this? Can anybody suggest a method to find out the missing tRNAs.
Is your sequence assembly reference based or de novo? Did you use whole genome sequencing or isolated mitochondrial genome and sequenced it? if you do have a reference genome then try using the tRNA sequences from it and BLAST against the contigs generated. If you find a hit then it could possibly be an assembly error.
Thank you Sudheesh for your reply. We did whole genome sequencing and did de novo assembly. we didnt have a refernce sequence.
The attached PDF discusses the mitochondrial complete genomes from dozens of frog species sampled across a wide range of different frogs. I looked at a few of them and they all had 2 copies of tRNA-Ser and one copy of tRNA-His, so it does seem unusual for them to be missing.
I have checked NCBI and usually tRNA-his and tRNA-ser come next to each other in the mitochondrial genomes of frogs. if you can find any closely related species from the NCBI organellar genome database (http://www.ncbi.nlm.nih.gov/genome/browse/?report=5) then you can take the sequences and run a blast against your contigs, you might possibly find both the sequences on the same contig.
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