MicroRNA Evolution

Tittle

• Conservation of MicroRNA genes across genomes

Objective

1. To study the miRNA similarity between species
2. miRNA as a classifier between species.
3. Defining common motifs/signature in miRNAs of human (Primary, Mature and Precursor)
4. A phylogenetic tree for miRNAs of Human, mouse and other species.
5. Possible subclassification of miRNAs.

Data

Kept in mustard /home/rajkumar/mirna/

• mature.fa - 4434 entries - 21 - 23 bases
• mirna precursor.txt - 4584 entries - ~ 60 - 130 bases

Programme

Search for mirna in Mimulus (from Mimulus unigenes)

1. Driving question
   1. Does miRNA really has phylogenetic signal across Asterids?
   2. If so, how far the miRNA is conserved/diverged?
   3. Conservation/divergence of Mimulus miRNAs
2. Data
   1. Unigenes from Arabidopsis,
   2. Tomato
   3. Rice
   4. Mimulus
   5. Populus
3. Plan of work
   1. Assemble ESTs and proteins of available systems
   2. Blast against protein database
   3. Remove the protein coding ESTS
   4. Again blast against EST database (0-4 mismatches)
   5. Predict the RNA structure by mfod 3.1
   6. Harpin Candidates
   7. Examine the annotations
   8. Noval potential miRNa genes
   9. Align the miRNA genes
   10. Perform phylogenetic analysis

Conservation of MicroRNA genes across genomes

1. Assemble the mature.fa with Plant and animal miRNA seq sorted out separately
2. Align the mature.fa sequences using Genome Threader or clustal family software
3. Find out the coordinates of most common motifs (might need to play with the stringency parameters a bit in alignment)
4. Might need a subclassifications, to visualize in Apollo

Related Articles

• Conservation and divergence of plant microRNA genes Plant J. 2006 Apr;46(2):243-59
• mirna protocols