@inbook {961266, title = {Comparative genomics as a foundation for evo-devo studies in birds}, booktitle = {Methods in Molecular Biology: Avian and Reptilian Developmental Biology}, year = {2017}, publisher = {Humana Press}, organization = {Humana Press}, address = {New York}, abstract = {

Developmental genomics is a rapidly growing field and high quality genomes are a useful foundation for comparative developmental studies. A genome streamlines and simplifies the development of primers used to isolate putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, micro RNAs (miRNAs) or short hairpin RNAs(shRNA) forRNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and in recent years, even guide RNAs (gRNAs) for CRISPR knockouts. A high quality genome also forms an essential reference onto which the data from numerous assays and experiments, including ChIPseq, ATAC-seq, and RNA-seq, can be mapped. Finally, much can be gleaned from comparative genomics alone, including 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.

}, author = {Phil Grayson and Simon Y W Sin and Tim Sackton and Edwards, S. V.} }