Supporting data for “Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building”
Dataset type: Genomic
Data released on March 23, 2018
Pomerantz A; Peñafiel N; Arteaga A; Bustamante L; Pichardo F; Coloma LA; Barrio-Amorós C; Salazar-Valenzuela D; Prost S (2018): Supporting data for “Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building” GigaScience Database. http://dx.doi.org/10.5524/100426
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 utilized portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcoding of reptile specimens in the field.
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 Universidad Tecnológica Indoamérica in Quito for rare, endangered, and undescribed species. This includes the recently re-discovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as little 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.
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 research by promoting local research capacity building, teaching laymen and students about the environment, tackling wildlife crime or by promoting conservation via research focused eco-tourism.
Additional details
Read the peer-reviewed publication(s):
(PubMed: 29617771)
Accessions (data generated as part of this study):
BioProject:
PRJNA438544
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
atelgn | 330826 | Atelopus ignescens | Description:DNA extract Jambato toad, Atelopus ign... Geographic location (latitude and longitude):not c... Elevation:not collected ... + | ||
Dipsas_MZUTI 5415 | 39144 | Dipsas | Description:DNA extract Snail eater snake, Dipsas ... Elevation:594 m Geographic location (country and/or sea,region):Ca... ... + | ||
Dipsas_MZUTI 5418 | 39144 | Dipsas | Description:DNA extract Snail eater snake, Dipsas ... Elevation:594 m Geographic location (country and/or sea,region):Ca... ... + | ||
Lep_aff_buc | 71157 | Lepidoblepharis | Description:DNA extract Dwarf gecko, Lepidoblephar... Elevation:594 m Geographic location (country and/or sea,region):Ca... ... + | ||
lep_aff_Gran1 | 71157 | Lepidoblepharis | Description:DNA extract Dwarf gecko, Lepidoblephar... Elevation:594 m Geographic location (country and/or sea,region):Ca... ... + | ||
pitViper1 | 44725 | Bothriechis schlegelii | Description:DNA extract Eyelash pit viper, Bothrie... Elevation:594 m Geographic location (country and/or sea,region):Ca... ... + | ||
sibon1 | 211650 | Sibon sp | Description:DNA extract Sibon snake, Dipsas sp, us... Elevation:594 m Geographic location (country and/or sea,region):Ca... ... + | ||
TriGua | 1334233 | Trilepida guayaquilensis | Description:DNA extract Blind snake, Trilepida gua... Elevation:594 m Geographic location (country and/or sea,region):Ca... ... + |