Identification of non-model mammal species using the MinION DNA sequencer from Oxford Nanopore DOI Creative Commons
Sara Velásquez Restrepo,

Mariana Corrales Orozco,

Nicolás D. Franco‐Sierra

et al.

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e17887 - e17887

Published: Sept. 25, 2024

Background The Neotropics harbors the largest species richness of planet; however, even in well-studied groups, there are potentially hundreds that lack a formal description, and likewise, many already described taxa difficult to identify using morphology. Specifically small mammals, complex morphological diagnoses have been facilitated by use molecular data, particularly from mitochondrial sequences, obtain accurate identifications. Obtaining markers implies PCR specific primers, which largely absent for non-model organisms. Oxford Nanopore Technologies (ONT) is new alternative sequencing entire genome without need primers. Only limited number studies employed exclusively ONT long-reads assemble genomes, few yet evaluated usefulness such reads multiple Methods We implemented fieldwork collect including rodents, bats, marsupials, five localities northern extreme Cordillera Central Colombia. DNA samples were sequenced MinION device Flongle flow cells. Shotgun-sequenced data was used reconstruct all samples. In parallel, customized computational pipeline, species-level identifications obtained based on raw (Whole Genome Sequencing). ONT-based corroborated traditional characters phylogenetic analyses. Results A total 24 individuals 18 collected, morphologically identified, deposited biological collection Universidad EAFIT. Our different pipelines able genomes reads. three eight sequences six species. identification pipeline up 75% as little 5 s. Finally, our analyses automated revealed important contributions knowledge diversity Neotropical mammals. Discussion This study evaluate organisms, reads, benchmarking these protocols multi-species dataset. proposed methodology can be applied non-expert taxonomists has potential real-time, euthanize organisms under field conditions. Therefore, it stands relevant tool help increase available rate at researchers characterize life specially highly biodiverse places Neotropics.

Language: Английский

Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology DOI
David Bass, Kevin W. Christison, Grant D. Stentiford

et al.

Trends in Parasitology, Journal Year: 2023, Volume and Issue: 39(4), P. 285 - 304

Published: Feb. 8, 2023

Language: Английский

Citations

47
ONTbarcoder 2.0: rapid species discovery and identification with real‐time barcoding facilitated by Oxford Nanopore R10.4 DOI Creative Commons
Amrita Srivathsan, Vivian Feng, Daniel Suárez

et al.

Cladistics, Journal Year: 2023, Volume and Issue: 40(2), P. 192 - 203

Published: Dec. 2, 2023

Abstract Most arthropod species are undescribed and hidden in specimen‐rich samples that difficult to sort using morphological characters. For such samples, sorting putative with DNA barcodes is an attractive alternative, but needs cost‐effective techniques suitable for use many laboratories around the world. Barcoding portable inexpensive MinION sequencer produced by Oxford Nanopore Technologies (ONT) could be useful presorting because it requires little space inexpensive. However, similarly important user‐friendly reliable software analysis of ONT data. It here provided form ONTbarcoder 2.0 all commonly used operating systems includes a Graphical User Interface (GUI). Compared earlier version, has three key improvements related higher read quality obtained ONT's latest flow cells (R10.4), chemistry (V14 kits) basecalling model (super‐accuracy model). First, improved (R10.4) allows primers shorter indices than those previously needed (9 bp vs. 12–13 bp). This decreases primer cost can potentially improve PCR success rates. Second, now delivers real‐time barcoding complement sequencing. means first within minutes starting sequencing run; i.e. cell optimized terminating runs when most have already been obtained. The only input demultiplexing sheet data (raw or basecalled) generated either Mk1B Mk1C. Thirdly, we demonstrate availability R10.4 low‐cost Flongle option users who require 200–250 at time.

Language: Английский

Citations

32
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples DOI Creative Commons
Cristina Vasiliţa, Vivian Feng, Aslak Kappel Hansen

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 19, 2024

The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, authenticating food. main reason that existing express workflows are either too expensive or can only be used very well-equipped laboratories by highly-trained staff. We here show an alternative workflow combining extraction with HotSHOT, amplicon production NextGenPCR thermocyclers, sequencing low-cost MinION sequencers. demonstrate the power approach generating 250 barcodes 285 specimens within 6 h including through BLAST. required following major equipment easily fits onto a lab bench: Thermocycler, NextGenPCR, microplate sealer, Qubit, MinION. Based on our results, we argue simplified species-level sorting now faster, more accurate, sufficiently cost-effective to replace traditional morpho-species many projects.

Language: Английский

Citations

10
Real‐time genomics for One Health DOI Creative Commons
Lara Urban, Albert Perlas, Olga Francino

et al.

Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(8)

Published: June 16, 2023

The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to future relationship planet. While the concept One Health describes how human health is inextricably linked health, many these complex interdependencies are still not well-understood. Here, we describe advent real-time genomic analyses can benefit it enable timely, in-depth ecosystem assessments. We introduce nanopore sequencing as only disruptive technology that currently allows for already being used worldwide improve accessibility versatility sequencing. showcase studies on zoonotic disease, food security, microbiome, emerging pathogens, their antimicrobial resistances, itself - from resource creation wildlife conservation monitoring biodiversity, invasive species, trafficking. stress why equitable access genomics in context will be paramount discuss related practical, legal, ethical limitations.

Language: Английский

Citations

22
Achieving zero extinction for land plants DOI Open Access
Richard T. Corlett

Trends in Plant Science, Journal Year: 2023, Volume and Issue: 28(8), P. 913 - 923

Published: May 2, 2023

Language: Английский

Citations

20
Harnessing the omics revolution to address the global biodiversity crisis DOI
Luis F. De León, Bruna Silva, Kevin J. Avilés‐Rodríguez

et al.

Current Opinion in Biotechnology, Journal Year: 2023, Volume and Issue: 80, P. 102901 - 102901

Published: Feb. 10, 2023

Language: Английский

Citations

19
The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research DOI Creative Commons

Chun-Miao Ji,

Xiao-Yin Feng,

Yao‐Wei Huang

et al.

Viruses, Journal Year: 2024, Volume and Issue: 16(5), P. 798 - 798

Published: May 16, 2024

In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well caused substantial economic losses. It is crucial understand the genomic structure epidemiology these guide effective clinical prevention treatment strategies. Nanopore sequencing, third-generation sequencing technology, has been widely used in research since 2014. This technology offers several advantages over traditional methods next-generation (NGS), such ability generate ultra-long reads, high efficiency, real-time monitoring analysis, portability, directly sequence RNA or DNA molecules. As result, it exhibits excellent applicability flexibility virus research, including viral detection surveillance, genome assembly, discovery new variants novel viruses, identification chemical modifications. this paper, we provide comprehensive review development, principles, advantages, applications nanopore aiming offer fresh perspectives for future studies field.

Language: Английский

Citations

7
REVOLUTIONIZING PLANT BREEDING PROGRAMS WITH ADVANCEMENTS IN MOLECULAR MARKER-ASSISTED SELECTION DOI Creative Commons
Asad Abbas,

Amna Arshad,

AU REHMAN

et al.

Bulletin of Biological and Allied Sciences Research, Journal Year: 2024, Volume and Issue: 2024(1), P. 57 - 57

Published: Jan. 4, 2024

The molecular marker method has come a long way in the last 30 years. Genetic research advanced from RFLPs to SNPs. Array technology was also used. Sequencing progress led creation of low-cost NGS systems with high throughput. Phenotyping been very important making this possible. Markers for crops like rice, corn, and potatoes have worked on, but markers that aren't used much haven't studied as much. Phylogenetics ecology are other areas don't know about markers. Plant breeding DNA modification greatly changed since recent improvements CRISPR technology. To contrary, some MAS (marker-assisted selection) methods need genome beforehand, which makes work even harder. Researchers plant science might find discussed review piece useful database. They could use them alone or sequence-level characters different fields.

Language: Английский

Citations

6
Metagenomic approaches and opportunities in arid soil research DOI
Muhammad Ejaz, Kareem Rady Badr, Zahoor Ul Hassan

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 953, P. 176173 - 176173

Published: Sept. 10, 2024

Language: Английский

Citations

5
Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community DOI Creative Commons
Amrita Srivathsan, Rebecca Ker Loh,

Elliott James Ong

et al.

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(23), P. 6418 - 6435

Published: Nov. 3, 2022

DNA obtained from invertebrates (iDNA) can be metabarcoded in order to survey vertebrate communities. However, little attention has been paid the interaction between invertebrate and species. Here, we tested for specialization by sampling dung carrion fly community of a swamp forest remnant along disturbance gradient (10 sites: 80-310 m road). Approximately, 60% baited 407 flies yielded 294 identifications based on two COI fragments 16S. A bipartite network analysis found no statistically significant interactions species, but uncommon species carry signal that are otherwise difficult detect with iDNA. spatial revealed most 20 reported this study could detected within 150 road (18 spp.) sourced iDNA was unexpectedly rich (24 3 families). They carried rare common inhabiting different layers (ground-dwelling: wild boar, Sunda pangolin, skinks, rats; arboreal: long-tailed macaque, Raffles' banded langur; flying: pin-striped tit-babbler, olive-winged bulbul). All our results were new, greatly simplified protocol eliminates extraction obtaining template directly through dissolving faeces regurgitates water. Lastly, show MinION- Illumina-based metabarcoding yield similar results. We conclude urging more studies use baits involve experiments capable revealing dispersal capabilities carrying

Language: Английский

Citations

21