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This volume focuses on the latest methods used to sequence, assemble, and analyze insect genomes. The collection of protocols in this book provides an introduction to the workflows and bioinformatics tools available for researchers. The chapters cover a range of useful topics such as determining genome size by flow cytometry; High Molecular Weight DNA extraction; improvements to a genome assembly provided by long-range sequencing approaches; assessments of orthology and single-copy genes at different phylogenetic levels; detecting regulatory regions with FAIRE, RAMPAGE, and computational analysis of cis-regulatory modules in insects; bioinformatics analysis of epigenetic modifications, high-throughput scanning of insect genomes (TEEseq) for the presence of endosymbionts, and leveraging genome sequence information to design RNAi strategies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Insect Genomics: Methods and Protocols is a valuable resource for graduate students, postdocs, and novice research scientists who are interested in learning more about this developing field.

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Chapter 1 Arthropod Genome Sequencing and Assembly Strategies

Chapter 2 Genome Size Estimation and Quantitative Cytogenetics in Insects

Chapter 3 Isolation of HMW DNA from Insects Chapter

Chapter 4 Long range sequencing and assembly QC

Chapter 5 Integrated modeling of structural genes using MCuNovo

Chapter 6 Using BUSCO to Assess Insect Genomic Resources

Chapter 7 The GFF3toolkit-QC and Merge Pipeline for Genome Annotation

Chapter 8 Using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) to identify functional regulatory DNA in insect genomes
Chapter 9 Using RAMPAGE to identify and annotate promoters in insect genomes

Chapter 10 CRM Beyond Model Insects

Chapter 11 Whole-genome bisulfite sequencing for the methylation analysis of insect genomes

Chapter 12 Bioinformatic analysis of methylation patterns using bisulfite sequencing data

Chapter 13 Physical Genome Mapping Using Fluorescence in Situ Hybridization with Mosquito Chromosomes

Chapter 14 Target enriched RAD sequencing (TEEseq): A new high-throughput sequencing approach applied to the comprehensive characterization of endosymbionts

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