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

DOI10.5524/100426

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):

Pomerantz, A., Peñafiel, N., Arteaga, A., Bustamante, L., Pichardo, F., Coloma, L. A., … Prost, S. (2018). Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building. GigaScience, 7(4). doi:10.1093/gigascience/giy033

Accessions (data included in GigaDB):

BioProject: PRJNA438544





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
atelgn330826  Atelopus ignescens Description:DNA extract Jambato toad, Atelopus ign...
Geographic location (latitude and longitude):not c...
Elevation:not collected
...
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Dipsas_MZUTI 541539144  Dipsas Description:DNA extract Snail eater snake, Dipsas ...
Geographic location (latitude and longitude):0.529...
Elevation:594 m
...
+
Dipsas_MZUTI 541839144  Dipsas Description:DNA extract Snail eater snake, Dipsas ...
Geographic location (latitude and longitude):0.529...
Elevation:594 m
...
+
Lep_aff_buc71157  Lepidoblepharis Description:DNA extract Dwarf gecko, Lepidoblephar...
Geographic location (latitude and longitude):0.529...
Elevation:594 m
...
+
lep_aff_Gran171157  Lepidoblepharis Description:DNA extract Dwarf gecko, Lepidoblephar...
Geographic location (latitude and longitude):0.529...
Elevation:594 m
...
+
pitViper144725  Bothriechis schlegelii Description:DNA extract Eyelash pit viper, Bothrie...
Geographic location (latitude and longitude):0.529...
Elevation:594 m
...
+
sibon1211650  Sibon sp Description:DNA extract Sibon snake, Dipsas sp, us...
Geographic location (latitude and longitude):0.529...
Elevation:594 m
...
+
TriGua1334233  Trilepida guayaquilensis Description:DNA extract Blind snake, Trilepida gua...
Geographic location (latitude and longitude):0.529...
Elevation:594 m
...
+
Displaying 1-8 of 8 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
mixed archivezip10.55 KB2018-03-20
Phylogenetic treeNewick6.34 KB2018-03-20
Phylogenetic treeNewick3.71 KB2018-03-20
Phylogenetic treeNewick3.97 KB2018-03-20
fastaTEXT5.51 KB2018-03-20
fastaFASTA7.42 KB2018-03-20
Phylogenetic treeNewick4.96 KB2018-03-20
Phylogenetic treeNewick6.67 KB2018-03-20
ReadmeTEXT2.87 KB2018-03-20
Displaying 1-9 of 9 File(s).
Funding body Awardee Award ID Comments
National Geographic Society A Pomerantz W412-15
Date Action
March 22, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy033