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

  • Phil Grayson
  • Simon Y. W. Sin
  • Timothy B. Sackton
  • Scott V. EdwardsEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1650)


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.

Key words

Genome assembly Library preparation Avian Bird Developmental genomics ALLPATHS-LG Comparative genomics 


  1. 1.
    Stern CD (2005) The chick: a great model system becomes even greater. Dev Cell 8:9–17PubMedGoogle Scholar
  2. 2.
    Nagai H, Mak S-S, Weng W et al (2011) Embryonic development of the emu, Dromaius novaehollandiae. Dev Dyn 240:162–175CrossRefPubMedGoogle Scholar
  3. 3.
    Padgett CS, Ivey WD (1960) The normal embryology of the coturnix quail. Anat Rec 137:1–11CrossRefPubMedGoogle Scholar
  4. 4.
    Murray JR, Varian-Ramos CW, Welch ZS et al (2013) Embryological staging of the Zebra Finch, Taeniopygia guttata. J Morphol 274:1090–1110CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Hillier LW, Miller W, Birney E et al (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716CrossRefGoogle Scholar
  6. 6.
    Zhang G, Li C, Li Q et al (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311–1320CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Jarvis ED, Mirarab S, Aberer AJ et al (2014) Whole genome analyses resolve the early branches in the tree of life of modern birds. Science 346:1320–1331CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Zhang G (2015) Bird sequencing project takes off. Nature 522:34CrossRefPubMedGoogle Scholar
  9. 9.
    Bonneaud C, Burnside J, Edwards SV (2008) High-speed developments in avian genomics. BioScience 58:587–595CrossRefGoogle Scholar
  10. 10.
    Gnerre S, Maccallum I, Przybylski D et al (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108:1513–1518CrossRefPubMedGoogle Scholar
  11. 11.
    Bradnam KR, Fass JN, Alexandrov A et al (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2:10CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Goodwin S, Gurtowski J, Ethe-Sayers S et al (2015) Oxford nanopore sequencing and de novo assembly of a eukaryotic genome. Genome Res 25(11):1750–1756CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics, Proteomics Bioinformatics 13:278–289CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Gordon D, Huddleston J, Chaisson MJ et al (2016) Long-read sequence assembly of the gorilla genome. Science 352:aae0344CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Mostovoy Y, Levy-Sakin M, Lam J et al (2016) A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 13:12–17CrossRefGoogle Scholar
  17. 17.
    Weisenfeld NI, Kumar V, Shah P et al (2017) Direct determination of diploid genome sequences. Genome Res 27(5):757–767CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Siepel A, Bejerano G, Pedersen JS et al (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15:1034–1050CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Visel A, Prabhakar S, Akiyama JA et al (2008) Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet 40:158–160CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Lowe CB, Kellis M, Siepel A et al (2011) Three periods of regulatory innovation during vertebrate evolution. Science (New York, NY) 333:1019–1024CrossRefGoogle Scholar
  21. 21.
    Lowe CB, Clarke JA, Baker AJ et al (2015) Feather development genes and associated regulatory innovation predate the origin of dinosauria. Mol Biol Evol 32:23–28Google Scholar
  22. 22.
    Marcovitz A, Jia R, Bejerano G (2016) “Reverse genomics” predicts function of human conserved noncoding elements. Mol Biol Evol 33:1358–1369CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Hiller M, Schaar BT, Bejerano G (2012) Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res 40:11463–11476CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Seki R, Li C, Fang Q, Hayashi S, Egawa S, Hu J, Xu L, Pan H, Kondo M, Sato T, Matsubara H, Kamiyama N, Kitajima K, Saito D, Liu Y, Thomas M, Gilbert P, Zhou Q, Xu X, Shiroishi T, Irie N, Tamura K, Zhang G (2017) Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nat Commun 8:14229CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Booker BM, Friedrich T, Mason MK et al (2016) Bat accelerated regions identify a bat forelimb specific enhancer in the HoxD Locus. PLoS Genet 12(3):e1005738Google Scholar
  26. 26.
    Eckalbar WL, Schlebusch SA, Mason MK et al (2016) Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet 48:528–536CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Domyan ET, Kronenberg Z, Infante CR et al (2016) Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. elife 5:1–21CrossRefGoogle Scholar
  28. 28.
    Adachi N, Robinson M, Goolsbee A et al (2016) Regulatory evolution of Tbx5 and the origin of paired appendages. Proc Natl Acad Sci 113:10115–10120CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Towns J, Cockerill T, Dahan M, Foster I, Gaither K, Grimshaw A, Hazlewood V, Lathrop S, Lifka D, Peterson GD, Roskies R, Ray Scott J, Wilkens-Diehr N (2014) XSEDE: accelerating scientific discovery. Comput Sci Eng 16(5):62–74CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Phil Grayson
    • 1
    • 2
  • Simon Y. W. Sin
    • 1
    • 2
  • Timothy B. Sackton
    • 3
  • Scott V. Edwards
    • 1
    • 2
    Email author
  1. 1.Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUSA
  2. 2.Museum of Comparative ZoologyHarvard UniversityCambridgeUSA
  3. 3.Informatics Group, Faculty of Arts and SciencesHarvard UniversityCambridgeUSA

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