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Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

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Department of Biogeography, University of Trier, 54296 Trier, Germany
2
Department of Integrative Biology, University of California, Berkeley, CA-94720, USA
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Marine Biology Laboratory, Woods Hole, MA-02543, USA
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LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, 60325 Frankfurt, Germany
5
South African National Biodiversity Institute, National Zoological Garden, Pretoria 0002, South Africa
*
Author to whom correspondence should be addressed.
Genes 2019, 10(11), 858; https://doi.org/10.3390/genes10110858
Received: 17 September 2019 / Revised: 18 October 2019 / Accepted: 25 October 2019 / Published: 29 October 2019
(This article belongs to the Special Issue MetaGenomics Sequencing In Situ)
We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology’s MinION portable sequencing platform, as well as summarize areas of recent development. View Full-Text
Keywords: portable sequencing; nanopore sequencing; biodiversity monitoring; local capacity building; MinION; DNA barcoding; long read sequencing portable sequencing; nanopore sequencing; biodiversity monitoring; local capacity building; MinION; DNA barcoding; long read sequencing
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Krehenwinkel, H.; Pomerantz, A.; Prost, S. Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions. Genes 2019, 10, 858.

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