Optimized and affordable high-throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens.

Molecular Ecology Resources
Jannik BenindeAxel Meyer

Abstract

Genomic analysis of hundreds of individuals is increasingly becoming standard in evolutionary and ecological research. Individual-based sequencing generates large amounts of valuable data from experimental and field studies, while using preserved samples is an invaluable resource for studying biodiversity in remote areas or across time. Yet, small-bodied individuals or specimens from collections are often of limited use for genomic analyses due to a lack of suitable extraction and library preparation protocols for preserved or small amounts of tissues. Currently, high-throughput sequencing in zooplankton is mostly restricted to clonal species, that can be maintained in live cultures to obtain sufficient amounts of tissue, or relies on a whole-genome amplification step that comes with several biases and high costs. Here, we present a workflow for high-throughput sequencing of single small individuals omitting the need for prior whole-genome amplification or live cultures. We establish and demonstrate this method using 27 species of the genus Daphnia, aquatic keystone organisms, and validate it with small-bodied ostracods. Our workflow is applicable to both live and preserved samples at low costs per sample. We first show that a ...Continue Reading

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Citations

Jun 25, 2021·PloS One·Samantha GunasekeraMark O'Dea
Jul 13, 2021·Molecular Ecology·Runyang Nicolas LouNina Overgaard Therkildsen

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