Literature DB >> 28337073

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer.

Sarah S Johnson1, Elena Zaikova2, David S Goerlitz3, Yu Bai2, Scott W Tighe4.   

Abstract

The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity. One-direction (1D) genomic libraries were prepared using portable field techniques on DNA isolated from desiccated microbial mats. By adequately insulating the sequencer and laptop, it was possible to run the sequencing protocol for up to 2½ h under arduous conditions.

Entities:  

Keywords:  Antarctica; MinION; Nanopore sequencing; extremophiles

Mesh：

Year:  2017        PMID： 28337073      PMCID： PMC5362188          DOI： 10.7171/jbt.17-2801-009

Source DB:  PubMed          Journal:  J Biomol Tech        ISSN： 1524-0215


  9 in total

1.  Long-term persistence of bacterial DNA.

Authors:  Eske Willerslev; Anders J Hansen; Regin Rønn; Tina B Brand; Ian Barnes; Carsten Wiuf; David Gilichinsky; David Mitchell; Alan Cooper
Journal:  Curr Biol       Date:  2004-01-06       Impact factor: 10.834

2.  Pint-sized DNA sequencer impresses first users.

Authors:  Erika Check Hayden
Journal:  Nature       Date:  2015-05-07       Impact factor: 49.962

Review 3.  A glimpse into past, present, and future DNA sequencing.

Authors:  Marcos Morey; Ana Fernández-Marmiesse; Daisy Castiñeiras; José M Fraga; María L Couce; José A Cocho
Journal:  Mol Genet Metab       Date:  2013-05-11       Impact factor: 4.797

Review 4.  Ten years of next-generation sequencing technology.

Authors:  Erwin L van Dijk; Hélène Auger; Yan Jaszczyszyn; Claude Thermes
Journal:  Trends Genet       Date:  2014-08-06       Impact factor: 11.639

5.  A first look at the Oxford Nanopore MinION sequencer.

Authors:  Alexander S Mikheyev; Mandy M Y Tin
Journal:  Mol Ecol Resour       Date:  2014-09-24       Impact factor: 7.090

Review 6.  Nanopore-based fourth-generation DNA sequencing technology.

Authors:  Yanxiao Feng; Yuechuan Zhang; Cuifeng Ying; Deqiang Wang; Chunlei Du
Journal:  Genomics Proteomics Bioinformatics       Date:  2015-03-02       Impact factor: 7.691

Review 7.  Oxford Nanopore MinION Sequencing and Genome Assembly.

Authors:  Hengyun Lu; Francesca Giordano; Zemin Ning
Journal:  Genomics Proteomics Bioinformatics       Date:  2016-09-17       Impact factor: 7.691

8.  MinION Analysis and Reference Consortium: Phase 1 data release and analysis.

Authors:  Camilla L C Ip; Matthew Loose; John R Tyson; Mariateresa de Cesare; Bonnie L Brown; Miten Jain; Richard M Leggett; Ewan Birney; David Buck; Sara Goodwin; Hans J Jansen; Justin O'Grady; Hugh E Olsen; David A Eccles; Vadim Zalunin; John M Urban; Paolo Piazza; Rory J Bowden; Benedict Paten; Solomon Mwaigwisya; Elizabeth M Batty; Jared T Simpson; Terrance P Snutch
Journal:  F1000Res       Date:  2015-10-15

9.  Real-time, portable genome sequencing for Ebola surveillance.

Authors:  Joshua Quick; Nicholas J Loman; Sophie Duraffour; Jared T Simpson; Ettore Severi; Lauren Cowley; Joseph Akoi Bore; Raymond Koundouno; Gytis Dudas; Amy Mikhail; Nobila Ouédraogo; Babak Afrough; Amadou Bah; Jonathan Hj Baum; Beate Becker-Ziaja; Jan-Peter Boettcher; Mar Cabeza-Cabrerizo; Alvaro Camino-Sanchez; Lisa L Carter; Juiliane Doerrbecker; Theresa Enkirch; Isabel Graciela García Dorival; Nicole Hetzelt; Julia Hinzmann; Tobias Holm; Liana Eleni Kafetzopoulou; Michel Koropogui; Abigail Kosgey; Eeva Kuisma; Christopher H Logue; Antonio Mazzarelli; Sarah Meisel; Marc Mertens; Janine Michel; Didier Ngabo; Katja Nitzsche; Elisa Pallash; Livia Victoria Patrono; Jasmine Portmann; Johanna Gabriella Repits; Natasha Yasmin Rickett; Andrea Sachse; Katrin Singethan; Inês Vitoriano; Rahel L Yemanaberhan; Elsa G Zekeng; Racine Trina; Alexander Bello; Amadou Alpha Sall; Ousmane Faye; Oumar Faye; N'Faly Magassouba; Cecelia V Williams; Victoria Amburgey; Linda Winona; Emily Davis; Jon Gerlach; Franck Washington; Vanessa Monteil; Marine Jourdain; Marion Bererd; Alimou Camara; Hermann Somlare; Abdoulaye Camara; Marianne Gerard; Guillaume Bado; Bernard Baillet; Déborah Delaune; Koumpingnin Yacouba Nebie; Abdoulaye Diarra; Yacouba Savane; Raymond Bernard Pallawo; Giovanna Jaramillo Gutierrez; Natacha Milhano; Isabelle Roger; Christopher J Williams; Facinet Yattara; Kuiama Lewandowski; Jamie Taylor; Philip Rachwal; Daniel Turner; Georgios Pollakis; Julian A Hiscox; David A Matthews; Matthew K O'Shea; Andrew McD Johnston; Duncan Wilson; Emma Hutley; Erasmus Smit; Antonino Di Caro; Roman Woelfel; Kilian Stoecker; Erna Fleischmann; Martin Gabriel; Simon A Weller; Lamine Koivogui; Boubacar Diallo; Sakoba Keita; Andrew Rambaut; Pierre Formenty; Stephan Gunther; Miles W Carroll
Journal:  Nature       Date:  2016-02-03       Impact factor: 69.504
  9 in total
  38 in total

1.  Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.

Authors:  Kaire Loit; Kalev Adamson; Mohammad Bahram; Rasmus Puusepp; Sten Anslan; Riinu Kiiker; Rein Drenkhan; Leho Tedersoo
Journal:  Appl Environ Microbiol       Date:  2019-10-16       Impact factor: 4.792

Review 2.  Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution.

Authors:  Débora Pires Paula
Journal:  Neotrop Entomol       Date:  2021-08-10       Impact factor: 1.434

Review 3.  Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations.

Authors:  Jesse J Salk; Michael W Schmitt; Lawrence A Loeb
Journal:  Nat Rev Genet       Date:  2018-03-26       Impact factor: 53.242

4.  De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads.

Authors:  David Eccles; Jodie Chandler; Mali Camberis; Bernard Henrissat; Sergey Koren; Graham Le Gros; Jonathan J Ewbank
Journal:  BMC Biol       Date:  2018-01-11       Impact factor: 7.431

Review 5.  Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment.

Authors:  Aaron Pomerantz; Kristoffer Sahlin; Nina Vasiljevic; Adeline Seah; Marisa Lim; Emily Humble; Susan Kennedy; Henrik Krehenwinkel; Sven Winter; Rob Ogden; Stefan Prost
Journal:  Nat Protoc       Date:  2022-04-11       Impact factor: 13.491

6.  Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.

Authors:  Rebecca Hooper; Jaelle C Brealey; Tom van der Valk; Antton Alberdi; John W Durban; Holly Fearnbach; Kelly M Robertson; Robin W Baird; M Bradley Hanson; Paul Wade; M Thomas P Gilbert; Phillip A Morin; Jochen B W Wolf; Andrew D Foote; Katerina Guschanski
Journal:  Mol Ecol       Date:  2018-10-24       Impact factor: 6.185

7.  In Situ Field Sequencing and Life Detection in Remote (79°26'N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities.

Authors:  J Goordial; Ianina Altshuler; Katherine Hindson; Kelly Chan-Yam; Evangelos Marcolefas; Lyle G Whyte
Journal:  Front Microbiol       Date:  2017-12-20       Impact factor: 5.640

8.  Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

Authors:  Sarah L Castro-Wallace; Charles Y Chiu; Kristen K John; Sarah E Stahl; Kathleen H Rubins; Alexa B R McIntyre; Jason P Dworkin; Mark L Lupisella; David J Smith; Douglas J Botkin; Timothy A Stephenson; Sissel Juul; Daniel J Turner; Fernando Izquierdo; Scot Federman; Doug Stryke; Sneha Somasekar; Noah Alexander; Guixia Yu; Christopher E Mason; Aaron S Burton
Journal:  Sci Rep       Date:  2017-12-21       Impact factor: 4.379

9.  Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol.

Authors:  Joseph A Russell; Brittany Campos; Jennifer Stone; Erik M Blosser; Nathan Burkett-Cadena; Jonathan L Jacobs
Journal:  Sci Rep       Date:  2018-04-03       Impact factor: 4.379

Review 10.  Understanding the role of the gut in undernutrition: what can technology tell us?

Authors:  Alex J Thompson; Claire D Bourke; Ruairi C Robertson; Nirupama Shivakumar; Christine A Edwards; Tom Preston; Elaine Holmes; Paul Kelly; Gary Frost; Douglas J Morrison
Journal:  Gut       Date:  2021-06-08       Impact factor: 23.059
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