March 26 @ 4:30 PM - 5:30 PM - ME 1130
Date: Tuesday, March 26, 2013
Time: 4:30 PM
Place: Mechanical Engineering (ME) 1130
Speaker: Arun Seetharam, Post-Doctoral Research Associate, Bioinformatics Core, Purdue University
Title: Next Gen Phylogenomics: An overview of nontraditional methods
Progress in the Next Generation Sequencing technologies have contributed to the accumulation of the sequence data for various organisms at an incredible pace. Phylogenomics, a term often used to describe the use of genomic scale data to infer species phylogeny or to predict protein function through evolutionary history, is greatly benefitted by this revolutionary progress. Standard methods for inferring phylogenetic relationships that involves multiple alignment of homologous sequences, followed by inference of a tree is no longer a feasible approach for phylogenomic studies. Here we will discuss numerous alternative approaches for building phylogenies that do not involve multiple sequence alignment. We will also present two case studies of phylogenomic methods on large genome-scale data. In the first study, we applied Singular Value Decomposition (SVD) analysis to re-examine current evolutionary relationships for 12 Drosophila species using the predicted proteins from whole
genomes. An SVD analysis on unfiltered whole genomes (193,622 predicted proteins) produced the currently accepted Drosophila phylogeny at higher dimensions, except for the generally accepted, but difficult to discern, sister relationship between D. erecta and D. yakuba. In the second study, we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species. Using the fragments generated by simulated digestion from the predicted targets of 16 Type IIB restriction enzymes, we sampled a large and effectively arbitrary selection of loci from these genomes. The resulting fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can improve studies !
of comparative genomics and the building of accurate phylogenetic trees.
Seetharam A, Stuart GW. 2012 Whole genome phylogenies for multiple Drosophila species. BMC research notes. 5:670. http://www.stat.purdue.edu/~doerge/BIOINFORM.D/SPRING13/SeetharamStuart2012BMCBioinf.pdf