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Phylogenetic Reconstruction based on RNA Secondary Structural Alignment. Benny Chor, Tel-Aviv Univ. Joint work with Moran Cabili, Assaf Meirovich, and Metsada Pasmanik-Chor. Phylogenetic Trees Based on What ? Morphology (1800 - ) Single gene sequence (DNA or AA) (1960 - ).

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## Phylogenetic Reconstruction based on RNA Secondary Structural Alignment

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**Phylogenetic Reconstruction based on RNA Secondary**Structural Alignment Benny Chor, Tel-Aviv Univ. Joint work with Moran Cabili, Assaf Meirovich, and Metsada Pasmanik-Chor**Phylogenetic TreesBased on What ?**• Morphology • (1800 - ) • Single gene sequence (DNA or AA) • (1960 - )**Phylogenetic TreesBased on What ?**• Whole genomes • (2002 - )**More Sources to Base Phylogeny On?**A Proposed, Metric Induced Approach • 1. Finda reliable metric between pairs of objects. • Design / choose / modify a good algorithm for determining metric (pairwise distances). • Compute distance matrix. • 4. Construct a Neighbor Joiningtree from the distance matrix. • 5. As a sanity check, compare resulting tree to • “standard & accepted” ones. NJ**Was already applied (fairly successfully), e.g.**for constructing phylogenies based on whole genomes/proteomes (Burstein et al., 2005), and others, based on metabolic networks (Tuller et al., 2006). • Metric Induced Approach NJ Of course distances that are appropriate to each domain must be applied (or especially designed).**Our Question**• Can phylogenetic reconstruction be based on RNA secondary structures ?**Our tree, based on**secondary structs. of 16s rRNA from 91 species Answer: Yes, And Even Quite Well Archaea Eukarya Bacteria**Metric Induced Approach: Specifics**• Find an efficient alignment algorithm • (similarity based) pair-wise RNA secondary • structures. • 2. Transform similarity to distance. • Use RNA databases to get the RNA molecules • and structures. Apply the algorithm to compute • the distance for each pair of molecules. • 4. Run NJ to produce trees.**The Alignment Algorithm Chosen**• We chose to use RSmatch: A sophisticated dynamic programming algorithm, based on the “dot bracket” representation of the secondary structure. • J. Liu , J.T. Wang , J. Hu , B. Tian. BMC Bioinformatics 2005 , 6:89. • RSmatch sorts each dot and bracket to components, and then compares components according to their order in the secondary structure. • RSmatch employs both sequences and structures. • Complexity: O(nm), where n and m are the lengths of the two RNA molecules that are compared. TAATTATCGGAAGCAGTGCCTTCCATAATTA ( ( ( ( ( ( ( . ( ( ( ( ( . . . . . . ) ) ) ) ) ) ) ) ) ) ) )**From Similarity to Distance**In transforming the scoring matrix from similarity to distance, we tried to preserve the ratios between mismatches values, and of course lower similarity should imply higher distance. Distance metric requirements: Symmetry, Δ inequality, non negativity, self distance=0**Actual Distance Matrices: Higher Mismatch Penalties at**“Dots” - Gap cost : 3 per nucleotide involved. - Δ inequality : mismatch < 2* gap cost**DBs constructed with manual intervention**• RNaseP DB: • http://www.mbio.ncsu.edu/RNaseP/ • Sequences length: ~300 - 400 (+/-) nucleotides RNaseP function: Cleaves off an extra, or precursor, sequence of RNA on tRNA molecules. • DBs of Reliable Secondary Struc. • 16S rRNA: • Comparative RNA Web Site: http://www.rna.icmb.utexas.edu/ • Sequences length: ~1,500 (+/-) nucleotides 16S function: In charge of tRNA binding and formation of peptide bonds during translation.**RNaseP Tree, 51 Species**• Secondary structure based tree • Good partition to 3 • kingdoms. • Bacteria • (characterized by • Bxy) also look good.**Eukarya**Bacteria • RNaseP 51 Species • Sequence based tree Archaea Eukaryotes are not monophyletic (yeast external).**Fungi**Mammalia Bacillariophyta Amphibia Viridaeplanatae 16s rRNA – 20 Species Secondary structure based tree**Archaea**Eukarya Bacteria 16s rRNA –91 Species Secondary structure based tree**Collins et al., 2000**• After completing this project, we discovered a related, earlier work from David Penny’s group. When determining evolutionary relationships between some catalytic RNA molecules, they constructed a 16S rRNA tree based on a similar “distance approach”. • We compared our results to • the trees published in their article • (using a different distance algorithm, • RNAdistance, by Shapiro & Zhang).**Collins’ 16s r RNA**secondary struct based tree Collins et al., 2000. Archaea Collins’ 16s rRNA sequence based tree 16 Species Archaea Bacteria Bacteria**Archaea**Bacteria Our Tree, 13 Out of 16 Collins’ Species Secondary structure based tree**A Close Look at the Trees**Collins’ 16s rRNA seq based tree outgroups Our 16s second. struct. tree Collins’ 16s second. struct. based tree**Methanobacteruim**Methanococcus Thermoplasma A Close Look at Sec. Strucs. Supports a “Thermoplasma Outgroup” Theory**Conclusions**• Encouraging results • Accuracy of structure based trees is comparable to sequence based trees. • Warning: Reliable secondary structures • are crucial for accurate tree reconstruction.

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