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Non-Coding RNAs


All the unigenes after assembly were searched for non-coding RNAs using different strategies. we identified tRNA encoding genes using command line version of tRNAscan-SE software. The rRNA encoding genes were predicted and classified using similarity search with Arabidopsis and Rice rRNA genes as well as using Rfam web server. The miRNA encoding genes were identified using similarity search with all plant miRNA sequences with stringent parameters.

  Details of Predicted Non-Coding RNAs
A. tRNA prediction   
tRNAs decoding Standard 20 AA   1167
Selenocysteine tRNAs (TCA) 5
Possible suppressor tRNAs (CTA,TTA) 1
tRNAs with undetermined/unknown isotypes  15
Predicted pseudogenes  144
Total tRNAs  1332
B. rRNA prediction 
Total rRNA sequences identified 587
Avg. Fragment size (bp) 107.4
Total bases classifed as rRNA (bp) 63056
C. miRNA prediction 
Total miRNA identified 78
Total length (bases) 1643
Total miRNA families identified 42
miRNA novel to Gossypium 17