1 / 7

Functionality of pack-mule sequences in Rice genome Kousuke Hanada 9/21/’06

Functionality of pack-mule sequences in Rice genome Kousuke Hanada 9/21/’06. Mutator -like transposable elements (MULEs) are DNA transposons that can be classified as either autonomous (transposase-encoding) or non-autonomous (not encoding but requiring transposase). Transposase. target.

chul
Download Presentation

Functionality of pack-mule sequences in Rice genome Kousuke Hanada 9/21/’06

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Functionality of pack-mule sequences in Rice genome Kousuke Hanada 9/21/’06

  2. Mutator-like transposable elements (MULEs) are DNA transposons that can be classified as either autonomous (transposase-encoding) or non-autonomous (not encoding but requiring transposase). Transposase target target site duplications insert Genomic region Duplication Interestingly, about 5,000 loci are duplicated in rice by this mechanism.

  3. Arg His Cys Ser Pro Met Sequence1 ATG AGG TGC TCT CCC CAC ・・・ Sequence2 ATG AGA TAC TCT CCC CAC ・・・ Tyr Arg Met Ser Pro His Purpose: To examine functionality of duplicated exon in pack-mule sequences Test of functionality : We can use selective pressure # nonsynonymous substitution / nucleotide site (Ka) Selective pressure= # synonymous substitution / nucleotide site (Ks) Ka <<1 : Functional constrain is strong Ks Ka = 1 : Functional constrain is week (Neutral) Ks

  4. Infer ancestor sequence Genomic sequences Pack-mule sequences Out group sequence Two selective pressures • Selective pressure (ka/ks ratio) between inferred ancestor sequence (●) andgenomic sequence • Selective pressure (ka/ks ratio) between inferred ancestor sequence (●)and pack-mule sequence If Ka/Ks ratio between inferred ancestor sequence and a pack-mule sequence is significantly less than 1, the pack-mule sequence has undergone strong functional constrain. the pack-mule sequence seems to be functional.

  5. Pipeline Pack-mule sequences Genomic sequences • Check whether genomic sequence includes coding region or not? • If yes  next step if no  end • Blastx between the protein sequence of genomic sequence and Pacl-mule sequences • Pack-mule sequences has six kids of frames for coding. • I defined a frame with the highest e-value as the frame of pack-mule. Blastx automatically produces the best alignments between coding region of genomic sequence and pack-mule sequence.(If stop codons existed in genomic sequence, I just removed the stop codon sites from both genomic and pack-mule sequences.) • If the total length of the aligbment is over 150bp (50aa)  next step • if no  end PackMule GCG GGA TAG GCG ACG GENOMIC GCG AGA TCG GCG ACG PackMule GCG GGA GCG ACG GENOMIC GCG AGA GCG ACG Remove

  6. Required condition for outgroup Genomic Sequences(G) Pack-mule sequences(P) Out group Sequence(O) Distance(G-O) > Distance(G-P) && Distance(P-O) > Distance (G-P) 3. Blastp search to all plant proteins (the protein sequence of genomic sequence as query) to get out group sequence 4. If the hit sequence is exactly match to genomic or pack-mule sequence, I did not use the sequence as outgroup 5. Construct alignment in genomic, pack-mule and putative outgroup sequences 5. Estimate synonymous distance (G-O, G-P, P-O) if(the distances do not have required conditions and remove the outgroup, go back to 3) If(the distances have required condition)we can get outgroup sequence

  7. Infer ancestor sequence Genomic Sequences(G) Pack-mule sequences(P) Out group Sequence(O) I estimate Ka and Ks distance in genomic lineage and pack-mule lineage. Although I got pipeline, I do not have all the data.

More Related