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Indian Institute of Science Education and Research Berhampur

BIO 425: Comparative and Evolutionary Genomics (OE, Credit, 3)

Course Content:

• Concepts in Genome Mining: Basic concepts and approaches in genome mining; varied approaches in comparative genomics analysis between the prokaryotic and eukaryotes,
• Phylogenomic approaches: Phylogenomic approaches in creating large-scale species trees (examples with Bacteria, Archaea, and Eukaryotes) and evolutionary dating; Alignment correction using statistical inference approaches and overcoming of tree artefacts. Estimation of phyletic profiles and approaches in tracing the evolution of gene families to LUCA (as well as Pre-LUCA), LECA and LHCA, among others;
• Comparative genomics approaches: Establishing functional landscape of gene families and systems using genomic contextual information (Gene neighborhoods); Retrieval of gene-neighborhoods in prokaryotes using PERL scripts; Functional network reconstruction using gene neighborhoods and protein domain architectures; Whole Genome alignment and Synteny inference; Identifying shared and unique genome content; Synteny to infer genome organization and constraint; Tools for Synteny computation and alignment; Orthology and Paralogy corrections using Synteny;
• Estimation of Lineage specific expansions and HGT events: Curation of lineage specific expansions of gene families and analysis using CAFÉ; Identification of horizontal gene transfer events using a standalone PERL Script;
• Functional divergence and Selection analysis: Estimation of functional divergence after gene duplication (Type-1 Divergence and Type-II divergence) using the Diverge software package; Estimating the rate of evolution in protein families using positional entropy analysis using R; Selection analysis on protein families and inferences on the evolution of structural scaffold;
• Arms-Race and Co-evolutionary trends: Using host and viral proteins as exemplars: Vertebrate viruses and estimation of viral diversification using phylogenomic approaches; Early vertebrate whole genome duplication and estimation of when and where novel genes arose; Arms-race between proteins deployed by vertebrate hosts and counter defense mechanisms by vertebrate viruses: How to study such Co- evolutionary trends of fast-evolving proteins?
• Genome annotation pipelines: NCBI Prokaryotic genome annotation pipelines; NCBI Eukaryotic genome annotation pipeline; Genome annotation pipelines such as Augustus, Maker and other pipelines.

Suggested Books:

• Sequence, Evolution, Function: Computational Approaches in Comparative Genomics. by Eugene V.
• Koonin and Michael Galperin.
• Introduction to Evolutionary Genomics, Saitou, Naruya
• Evolution by Gene Duplication. Susumu Ohno
• Evolutionary Genomics and Systems Biology, Editor(s): Gustavo Caetano‐Anollés
• Statistical Theory and Methods for Evolutionary Genomics. Xun Gu
• Evolutionary Systems Biology. Editors: Soyer, Orkun S. (Ed.)
• Phylogenomics An Introduction by Christoph Bleidorn
• Evolutionary Genomics Statistical and Computational Methods, Volume 2 Editors: Anisimova, Maria (Ed.)
• Foundations of Comparative Genomics. Arcady R. Mushegian (Author). Academic Press; 1st edition (24 May 2007)

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