title: Fundamentals of Comparative Genome Analysis in Caenorhabditis Nematodes.
abstract: The genome of the nematode Caenorhabditis elegans was the first of any animal to be sequenced completely, and it remains the "gold standard" for completeness and annotations. Even before the C. elegans genome was completed, however, biologists began examining the generality of its features in the genomes of other Caenorhabditis species. With many such genomes now sequenced and available via WormBase, C. elegans researchers are often confronted with how to interpret comparative genomic data. In this article, we present practical approaches to addressing several common issues, including possible sources of error in homology annotations, the often complex relationships between sequence similarity, orthology, paralogy, and gene family evolution, the impact of sexual mode on genome assemblies and content, and the determination and use of synteny as a tool.
authors.affiliation: Department of Biology, University of Maryland, 1210 Biology-Psychology Building, College Park, MD, 20742, USA. ehaag@umd.edu.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Haag
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada, M5S 3B2.
authors.forename: Cristel G
authors.initials: CG
authors.lastname: Thomas
mesh_terms: D000818:Animals; D002107:Caenorhabditis / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D018628:Gene Dosage; D049751:Genome, Helminth; D023281:Genomics / Q000379:methods*; D005838:Genotype; D010802:Phylogeny
keywords: Comparative genomics; Homology; Ortholog; Paralog; Phylogeny