Environmental DNA : for biodiversity research and monitoring / Pierre Taberlet, Aurélie Bonin, Lucie Zinger, Eric Coissac.

Format:

• Book

Author/Creator:

• Taberlet, Pierre.

Contributor:

• UPSO (University Press Scholarship Online)
• Rudolph G. Schmieder Fund.

Language:

English

Subjects (All):

• Ecological genetics.
• Metagenomics.
• Genomes--Analysis.
• Gene expression--Analysis.
• Gene expression.
• Genomes.

Physical Description:

• 1 online resource (272 pages)
• polychrome

Edition:

First Edition.

Place of Publication:

Oxford, United Kingdom : Oxford University Press 2018.

System Details:

text file

Contents:

• Cover; Contents; Acknowledgments; 1 Introduction to environmental DNA (eDNA); 1.1 Definitions; 1.2 A brief history of eDNA analysis; 1.3 Constraints when working with eDNA; 1.4 Workflow in eDNA studies and main methods used; 1.5 Environmental DNA as a monitoring tool; 2 DNA metabarcode choice and design; 2.1 Which DNA metabarcode?; 2.2 Properties of the ideal DNA metabarcode; 2.3 In silico primer design and testing; 2.3.1 Prerequisites; 2.3.2 R eference sequences: description,filtering, and formatting for ecoPrimers; 2.3.3 In silico primer design with ecoPrimers; 2.3.3.1 The ecoPrimers output
• 2.3.4 In silico primer testing with ecoPCR2.3.4.1 The ecoPCR output; 2.3.4.2 Filtering of the ecoPCR output; 2.3.4.3 Evaluation of primer conservation; 2.3.4.4 Taxonomic resolution and Bs index; 2.4 Examples of primer pairs available for DNA metabarcoding; 3 Reference databases; 3.1 Extracting reference databases from EMBL/GenBank/DDBJ; 3.1.1 Downloading a local copy of EMBL; 3.1.2 Identifying sequences corresponding to the relevant metabarcode; 3.2 Marker-specific reference databases; 3.2.1 Nuclear rRNA gene reference databases; 3.2.2 Eukaryote-specific databases
• 3.3 Building a local reference database3.3.1 PCR-based local reference database; 3.3.2 Shotgun-based local reference database; 3.4 Current challenges and future directions; 4 Sampling; 4.1 The cycle of eDNA in the environment; 4.1.1 State and origin; 4.1.2 Fate; 4.1.3 Transport; 4.2 Sampling design; 4.2.1 Focusing on the appropriate DNA population; 4.2.2 Defining the sampling strategy; 4.3 Sample preservation; 5 DNA extraction; 5.1 From soil samples; 5.2 From sediment; 5.3 From litter; 5.4 From fecal samples; 5.5 From water samples; 6 DNA amplification and multiplexing
• 6.1 Principle of the PCR6.2 Which polymerase to choose?; 6.3 The standard PCR reaction; 6.4 The importance of including appropriate controls; 6.4.1 Extraction negative controls; 6.4.2 PCR negative controls; 6.4.3 PCR positive controls; 6.4.4 Tagging system controls; 6.4.5 Internal controls; 6.5 PCR optimization; 6.6 How to limit the risk of contamination?; 6.7 Blocking oligonucleotides for reducing the amplification of undesirable sequences; 6.8 How many PCR replicates?; 6.9 Multiplexing several metabarcodes within the same PCR; 6.10 Multiplexing many samples on the same sequencing lane
• 6.10.1 Overview of the problem6.10.2 Strategy 1: single-step PCR with Illumina adapters; 6.10.3 Strategy 2: two-step PCR with Illumina adapters; 6.10.4 Strategy 3: single-step PCR with tagged primers; 7 DNA sequencing; 7.1 Overview of the first, second, and third generations of sequencing technologies; 7.2 The Illumina technology; 7.2.1 Library preparation; 7.2.2 Flow cell, bridge PCR, and clusters; 7.2.3 Sequencing by synthesis; 7.2.4 Quality scores of the sequence reads; 8 DNA metabarcoding data analysis; 8.1 Basic sequence handling and curation; 8.1.1 Sequencing quality

Notes:

• Includes bibliographical references and index.
• Electronic reproduction. Oxford Available via World Wide Web.
• Description based on online resource; title from digital title page (viewed on April 06, 2018).

Local Notes:

Acquired for the Penn Libraries with assistance from the Rudolph G. Schmieder Fund.

Other Format:

Print version: Taberlet, Pierre. Environmental DNA. For biodiversity research and monitoring.

ISBN:

• 9780191079993
• 0191079995
• 9780191821387
• 0191821381

Publisher Number:

99976596062

Access Restriction:

Restricted for use by site license.

Online:

The Rudolph G. Schmieder Fund Home Page