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Fundamentals of Comparative Genome Analysis in Caenorhabditis Nematodes

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Book cover C. elegans

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1327))

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.

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Authors and Affiliations

  1. Department of Biology, University of Maryland, 1210 Biology-Psychology Building, College Park, MD, 20742, USA

    Eric S. Haag

  2. Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada, M5S 3B2

    Cristel G. Thomas

Authors
  1. Eric S. Haag
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  2. Cristel G. Thomas
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Corresponding author

Correspondence to Eric S. Haag .

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Editors and Affiliations

  1. Department of Physics, The James Franck Institution, The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA

    David Biron

  2. Federated Department of Biological Sciences, New Jersey Institute of Technology and Rutgers University, Newark, New Jersey, USA

    Gal Haspel

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Haag, E.S., Thomas, C.G. (2015). Fundamentals of Comparative Genome Analysis in Caenorhabditis Nematodes. In: Biron, D., Haspel, G. (eds) C. elegans. Methods in Molecular Biology, vol 1327. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-4939-2842-2_2

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  • DOI: https://doi.org/10.1007/978-1-4939-2842-2_2

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-4939-2841-5

  • Online ISBN: 978-1-4939-2842-2

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