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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References
Stern CD (2005) The chick: a great model system becomes even greater. Dev Cell 8:9–17
Nagai H, Mak S-S, Weng W et al (2011) Embryonic development of the emu, Dromaius novaehollandiae. Dev Dyn 240:162–175
Padgett CS, Ivey WD (1960) The normal embryology of the coturnix quail. Anat Rec 137:1–11
Murray JR, Varian-Ramos CW, Welch ZS et al (2013) Embryological staging of the Zebra Finch, Taeniopygia guttata. J Morphol 274:1090–1110
Hillier LW, Miller W, Birney E et al (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716
Zhang G, Li C, Li Q et al (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346:1311–1320
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 346:1320–1331
Zhang G (2015) Bird sequencing project takes off. Nature 522:34
Bonneaud C, Burnside J, Edwards SV (2008) High-speed developments in avian genomics. BioScience 58:587–595
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 108:1513–1518
Bradnam KR, Fass JN, Alexandrov A et al (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2:10
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
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):1750–1756
Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics, Proteomics Bioinformatics 13:278–289
Gordon D, Huddleston J, Chaisson MJ et al (2016) Long-read sequence assembly of the gorilla genome. Science 352:aae0344
Mostovoy Y, Levy-Sakin M, Lam J et al (2016) A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 13:12–17
Weisenfeld NI, Kumar V, Shah P et al (2017) Direct determination of diploid genome sequences. Genome Res 27(5):757–767
Siepel A, Bejerano G, Pedersen JS et al (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15:1034–1050
Visel A, Prabhakar S, Akiyama JA et al (2008) Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet 40:158–160
Lowe CB, Kellis M, Siepel A et al (2011) Three periods of regulatory innovation during vertebrate evolution. Science (New York, NY) 333:1019–1024
Lowe CB, Clarke JA, Baker AJ et al (2015) Feather development genes and associated regulatory innovation predate the origin of dinosauria. Mol Biol Evol 32:23–28
Marcovitz A, Jia R, Bejerano G (2016) “Reverse genomics” predicts function of human conserved noncoding elements. Mol Biol Evol 33:1358–1369
Hiller M, Schaar BT, Bejerano G (2012) Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res 40:11463–11476
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 8:14229
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):e1005738
Eckalbar WL, Schlebusch SA, Mason MK et al (2016) Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet 48:528–536
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 5:1–21
Adachi N, Robinson M, Goolsbee A et al (2016) Regulatory evolution of Tbx5 and the origin of paired appendages. Proc Natl Acad Sci 113:10115–10120
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):62–74
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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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