Standardized biodiversity assessments using next-generation sequencing

Background: DNA barcoding is a powerful tool for cataloging biodiversity. While Malaise traps are commonly used to assess insect diversity, traditional approaches used to identify Malaise trap specimens are time consuming and, despite the substantial reduction of Sanger sequencing costs, remains exp...

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Bibliographic Details
Published inGenome Vol. 60; no. 11; p. 915
Main Authors Braukmann, Thomas W, Ivanova, Natalia V, Prosser, Sean, Sones, Jayme, deWaard, Jeremy R, Zakharov, Evgeny V
Format Journal Article
LanguageEnglish
Published Ottawa Canadian Science Publishing NRC Research Press 01.11.2017
Subjects
Assessments
Bias
Biodiversity
Comparative analysis
Cost analysis
Deoxyribonucleic acid
DNA
DNA polymerase
DNA sequencing
DNA-directed DNA polymerase
Error analysis
Fragmentation
Fragments
Genera
Genomics
Insects
Insertion
Lysis
Malaise trap
Polymerase chain reaction
Recovery
Sample preparation
Taxonomy
Traps
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Summary:Background: DNA barcoding is a powerful tool for cataloging biodiversity. While Malaise traps are commonly used to assess insect diversity, traditional approaches used to identify Malaise trap specimens are time consuming and, despite the substantial reduction of Sanger sequencing costs, remains expensive. Next-generation sequencing (NGS) can reduce the cost and time burden to analyze Malaise trap samples, and lead to the rapid assessment of insect biodiversity using a metagenomic approach. We compare the taxonomic resolution of fragments of different length using the Illumina MiSeq and Ion Torrent (PGM and S5) platforms. We also analyse the effect of tissue type, lysis time, and DNA polymerase on species recovery and (or) sequencing error rate. Results: This study demonstrates that longer barcoding fragments (i.e., 462 vs. 407 bp) improves taxonomic resolution in metagenomic samples. Illumina MiSeq reads have lower rates of insertion and deletion errors than the more cost efficient Ion torrent, but the error rate of the latter is reduced with the use of a high-fidelity polymerase. Ion torrent and Illumina have similar specimen recovery and coverage and most specimens were recovered with a subset of 150 000 reads. There is no difference in specimen recovery from different tissue types (leg or abdomen), but PCR bias is prevalent in pooled DNA sources with a few specimens dominating read coverage (<1000x). There are few differences in genera recovery between different lysis times of 1 h (91.8%), 2 h (91.3%), 4 h (93.25%), 8 h (89.9%), 16 h (94.2%), and 32 h (93.25%). Significance: This study highlights the influence of barcode fragment length on taxonomic resolution for metagenomic studies. The method of sample preparation(bulk vs. individual lysis) influences the effect of primer bias on diverse taxonomic samples. This work develops standardized protocol for inventorying insect biodiversity using Malaise traps.
ISSN:0831-2796
1480-3321