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Full Description
This volume covers the latest advancements and methods used to study DNA barcoding. The chapters in this book are organized into six parts: theory, DNA manipulation, specialized barcoding methods, analysis of DNA barcodes, completing a successful DNA barcode project, and barcoding as citizen science. Part One looks at several theoretical issues in DNA barcoding concerned with DNA barcodes that can and should be used. Part Two discusses protocols for processing samples into DNA barcodes, including DNA isolation, sequencing and managing samples, and the resulting DNA barcodes. Part Three explores the next generation of DNA barcoding such as FRET-based detection, dual nanopore detection, skimming, and closed-tube methods. Part Four addresses programs and websites that handle DNA barcoding data, and includes character-based approaches, barcode gap methods, integrated approaches, and Barcode of Life Database. Part Five offers protocols for producing a successfulDNA barcoding project including plant and animal examples and protocols for generating a DNA Barcode Reference Library. Lastly, Part Six talks about several novel protocols for setting up an educational program using DNA barcodes. 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, DNA Barcoding: Methods and Protocols encompasses a wide range of techniques and will be a useful reference tool for both scientist and student.
Contents
Part I DNA Barcoding Theory and Practice.- Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy.- Species Diagnosis and DNA Taxonomy.- Delimiting Species with Single-Locus DNA Sequences.- DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy.- DNA Barcodes in Taxonomic Descriptions.- Part II DNA Manipulation and Sequencing.- Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.- Cost-Effective DNA Extraction for DNA Barcoding Diverse Biological Sample.- DNA Sequencing Technologies and DNA Barcoding.- DNA Barcoding and Metabarcoding Protocols for Species Identification.- Environmental DNA Isolation, Validation, and Preservation Methods.- Part III Specialized DNA Barcoding Methods.- Single-Molecule FRET-Based Multiplexed Detection.- DNA Barcodes using a Dual Nanopore Device.- ddRAD Sequencing and DNA Barcoding.- Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing.- Generating 2D Barcode for DNA Barcode Sequences.- Analyses of Nuclear Reads Obtained using Genome Skimming.- Recent Advances in Closed-Tube Barcoding for FastFish-ID.- Part IV Analyzing DNA Barcode Data.- iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2.- DNA Barcode-Based Species Diagnosis with MolD.- Species Delimitation and Exploration of Species Partitions with ASAP and LIMES.- Characteristic Attribute Organization System (CAOS): Identifying Classification Rules Based on Phylogenetically Organized Sequences.- CAOS-R: Character-Based Barcoding.- Classification of DNA Sequence Based on a Non-Gradient Algorithm: Pseudoinverse Learners.- A Measure of the DNA Barcode Gap for Applied and Basic Research.- Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases.- BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.- Part V Generating a Successful DNA Barcode Project.- Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants.- MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.- Principles for Constructing DNA Barcode Reference Libraries.- Recent Applications of FastFish-ID.- Part VI DNA Barcoding, Teaching, and Citizen Science.- A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding.- Engaging Students and Teachers as Community Scientists in DNA Barcoding Initiatives.- DNA Barcoding for an Undergraduate Class.- Analysis of DNA Barcodes Using DNA Subway.- A Glossary of DNA Barcoding Terms.
