Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (GigaScience)
Abstract
Background
Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack in one of the world's most imperiled biodiversity hotspots, the Ecuadorian Chocó rainforest. We used portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, polymerase chain reaction amplification, and real-time DNA barcoding of reptile specimens in the field.
Findings
We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. The flexibility of our mobile laboratory further allowed us to generate sequence information at the Universidad Tecnológica Indoamérica in Quito for rare, endangered, and undescribed species. This includes the recently rediscovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as few as 30 reads to achieve high accuracy relative to Sanger sequencing, and with further multiplexing of samples, nanopore sequencing can become a cost-effective approach for rapid and portable DNA barcoding.
Conclusions
Overall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.
Article activity feed
-
Now published in GigaScience doi: 10.1093/gigascience/giy033
Aaron Pomerantz 1Department of Integrative Biology, University of California, Berkeley, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Pomerantz_aaron@berkeley.edu stprost@stanford.eduNicolás Peñafiel 2Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLucas Bustamante 3Tropical Herping, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFrank Pichardo 3Tropical …
Now published in GigaScience doi: 10.1093/gigascience/giy033
Aaron Pomerantz 1Department of Integrative Biology, University of California, Berkeley, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Pomerantz_aaron@berkeley.edu stprost@stanford.eduNicolás Peñafiel 2Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLucas Bustamante 3Tropical Herping, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFrank Pichardo 3Tropical Herping, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLuis A. Coloma 4Centro Jambatu de Investigación y Conservación de Anfibios, Fundación Otonga, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCésar L. Barrio-Amorós 5Doc Frog Expeditions, Uvita, Costa RicaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Salazar-Valenzuela 2Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, EcuadorFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStefan Prost 1Department of Integrative Biology, University of California, Berkeley, CA, USA6Program for Conservation Genomics, Department of Biology, Stanford University, Stanford, CA, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: Pomerantz_aaron@berkeley.edu stprost@stanford.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy033 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101071 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101072
-
-
