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Avian and Reptilian Developmental Biology pp 11–46Cite as

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1650))

Abstract

Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts. Finally, much can be gleaned from comparative genomics alone, including the identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high-quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments.

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Authors and Affiliations

  1. Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA

    Phil Grayson, Simon Y. W. Sin & Scott V. Edwards

  2. Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA

    Phil Grayson, Simon Y. W. Sin & Scott V. Edwards

  3. Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA

    Timothy B. Sackton

Authors
  1. Phil Grayson
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  2. Simon Y. W. Sin
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  3. Timothy B. Sackton
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  4. Scott V. Edwards
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Corresponding author

Correspondence to Scott V. Edwards .

Editor information

Editors and Affiliations

  1. IRCMS, Kumamoto University, Kumamoto, Kumamoto, Japan

    Guojun Sheng

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Grayson, P., Sin, S.Y.W., Sackton, T.B., Edwards, S.V. (2017). Comparative Genomics as a Foundation for Evo-Devo Studies in Birds. In: Sheng, G. (eds) Avian and Reptilian Developmental Biology. Methods in Molecular Biology, vol 1650. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7216-6_2

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  • DOI: https://doi.org/10.1007/978-1-4939-7216-6_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7215-9

  • Online ISBN: 978-1-4939-7216-6

  • eBook Packages: Springer Protocols

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