Comparing PCR-generated artifacts of different polymerases for improved accuracy of DNA metabarcoding

By

Nagai, Satoshi
Sildever, Sirje
Nishi, Noriko
Tazawa, Satoshi
Basti, Leila
Kobayashi, Takanori
Ishino, Yoshizumi

Type

Article

Date of Publication

2022-2-21

Original Publication

Metabarcoding and metagenomics

Volume

6

Pages

1--13

Subjects

18S rRNA gene , chimeric sequences , DNA polymerase , high throughput sequencing , metabarcoding , PCR-generated artifacts

Contributed by

Pensoft Publishers

Language

English

Published by

Bulgaria Pensoft Publishers 2017-

Identifiers

DOI: https://doi.org/10.3897/mbmg.6.77704

 

Abstract

Accuracy of PCR amplification is vital for obtaining reliable amplicon-sequencing results by metabarcoding. Here, we performed a comparative analysis of error profiles in the PCR products by 14 different PCR kits using a mock eukaryotic community DNA sample mimicking metabarcoding analysis. To prepare a mock eukaryotic community from the marine environment, equal amounts of plasmid DNA from 40 microalgal species were mixed and used for amplicon-sequencing by a high-throughput sequencing approach. To compare the differences in PCR kits used for this experiment, we focused on the following seven parameters: 1) Quality, 2) Chimera, 3) Blast top hit accuracy, 4) Deletion, 5) Insertion, 6) Base substitution and 7) Amplification bias amongst species. The results showed statistically significant differences (p < 0.05) for all of the seven parameters depending on the PCR kits used. These differences may result from the different DNA polymerases included in each kit, although the result can also be influenced by PCR reaction conditions. Simultaneous analysis of several parameters suggested that kits containing KOD plus Neo (TOYOBO) and HotStart Taq DNA polymerase (BiONEER, CA, US) at the annealing temperature of 65 °C displayed better results in terms of parameters associated with chimeras, top hit similarity and deletions.