2018
DOI: 10.1111/1755-0998.12888
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Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples

Abstract: New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR-free whole mitochondrial genome (mitogenome) sequencing may provide a more reliable alternative. Here, we used a set of documented mock communities comprising 13 species of freshwater macroinve… Show more

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Cited by 112 publications
(120 citation statements)
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“…Increasingly, these methods are also being used to quantify prey consumption although quantification can be considerably more challenging (Frischer et al, ; Nejstgaard et al, ). Results from NGS studies are particularly prone to systematic bias associated with library preparation, sequencing and bioinformatics procedures, and thus, it is recommended that NGS data be interpreted qualitatively unless appropriate controls or complimentary orthogonal methods are also applied (Bista et al, ; Hardwick, Deveson, & Mercer, ). In this study, NGS data were interpreted semi‐quantitatively and, in the case of diatoms, the results confirmed independently by real‐time qPCR.…”
Section: Discussionmentioning
confidence: 99%
“…Increasingly, these methods are also being used to quantify prey consumption although quantification can be considerably more challenging (Frischer et al, ; Nejstgaard et al, ). Results from NGS studies are particularly prone to systematic bias associated with library preparation, sequencing and bioinformatics procedures, and thus, it is recommended that NGS data be interpreted qualitatively unless appropriate controls or complimentary orthogonal methods are also applied (Bista et al, ; Hardwick, Deveson, & Mercer, ). In this study, NGS data were interpreted semi‐quantitatively and, in the case of diatoms, the results confirmed independently by real‐time qPCR.…”
Section: Discussionmentioning
confidence: 99%
“…Universal primers do not perfectly match the DNA of all species, and so there is a variable number of template-primer mismatches across species. In consequence, some species are better amplified than others and the proportions in the final mixture do not reflect the original proportion of each species (Bista et al, 2018;Elbrecht & Leese, 2015;Leray et al, 2013). There are other complications in the PCR step that produce more biases; for instance, the use of indexed PCR primers (used to minimize the per sample cost of sequencing by allowing the sequencing of many samples in a single run) might induce further biases (Leray & Knowlton, 2017;O'Donnell, Kelly, Lowell, & Port, 2016).…”
Section: Introductionmentioning
confidence: 99%
“…There are other complications in the PCR step that produce more biases; for instance, the use of indexed PCR primers (used to minimize the per sample cost of sequencing by allowing the sequencing of many samples in a single run) might induce further biases (Leray & Knowlton, 2017;O'Donnell, Kelly, Lowell, & Port, 2016). The avoidance of the PCR step (shotgun metagenomics) would in theory render a faithful list of R i (Bista et al, 2018), and this is what is mostly used in microbial metabarcoding nowadays (Jovel et al, 2016). However, in eukaryotes, the scarcity of assembled genomes, and the vast amount of sequencing depth needed, makes shotgun metabarcoding still unsuitable in most circumstances (Gómez-Rodríguez, Crampton-Platt, Timmermans, Baselga, & Vogler, 2015;Zhou et al, 2013).…”
Section: Introductionmentioning
confidence: 99%
“…Metabarcoding generates enormous biodiversity information of zooplankton with high sensitivity, including species at any stages, and cryptic species and organisms that are either too fragile, small or rare to be identified by traditional methods (Abad et al, 2016;Lindeque, Parry, Harmer, Somerfield, & Atkinson, 2013;Zhan et al, 2013). Thus, metabarcoding can comprehensively characterize taxa composition and estimate relative abundance of taxa in a semiquantitative way (Abad et al, 2016;Bista et al, 2018). As a result, metabarcoding-based methods have been popularly utilized in many ecological studies.…”
mentioning
confidence: 99%