DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

Bulletin of Entomological Research
G-J Brandon-MongJ-J Wilson

Abstract

Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units)...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jul 27, 2001·Applied and Environmental Microbiology·K Ishii, M Fukui
Mar 5, 2003·Proceedings. Biological Sciences·Paul D N HebertJeremy R deWaard
Oct 7, 2004·Proceedings of the National Academy of Sciences of the United States of America·Paul D N HebertWinnie Hallwachs
Oct 11, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·M Alex SmithPaul D N Hebert
Dec 1, 2006·The Journal of Heredity·Daniel RubinoffKipling Will
Apr 22, 2008·Nucleic Acids Research·A DereeperO Gascuel
May 14, 2008·BMC Genomics·Isabelle MeusnierMehrdad Hajibabaei
Aug 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·M Alex SmithPaul D N Hebert
Sep 2, 2008·Proceedings of the National Academy of Sciences of the United States of America·Hojun SongKeith A Crandall
Sep 12, 2008·Molecular Ecology Notes·Sujeevan Ratnasingham, Paul D N Hebert
Aug 28, 2010·Bioinformatics·Darren P MartinPierre Lefeuvre
Feb 19, 2011·Annual Review of Marine Science·Ann BucklinLeocadio Blanco-Bercial
Mar 25, 2011·Molecular Ecology Resources·Matt R K ZealeGareth Jones
Apr 12, 2011·PloS One·Hironori FujitaMasayoshi Kawaguchi
Mar 1, 2008·Molecular Ecology Resources·M Alex SmithPaul D N Hebert
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Apr 11, 2012·Molecular Ecology·Eric CoissacNicolas Puillandre
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
Apr 2, 2013·Journal of Microbiological Methods·Julia L StevensJulie B Olson
May 3, 2013·PloS One·Anna MummertXiu-Feng Wan
Oct 18, 2013·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Oct 22, 2013·Bioinformatics·Jiajie ZhangAlexandros Stamatakis
Nov 10, 2013·Journal of Applied Genetics·Živa Fišer Pečnikar, Elena V Buzan
Mar 13, 2014·PloS One·Maurijn Y KesselsSacco C de Vries
Apr 23, 2014·Molecular Ecology Resources·Laurence J ClarkeAlan Cooper

❮ Previous
Next ❯

Citations

Jan 12, 2016·Biodiversity Data Journal·John-James WilsonKong-Wah Sing
Jun 22, 2016·Genome Génome / Conseil National De Recherches Canada·Kong-Wah SingJohn-James Wilson
Aug 3, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Scott E MillerDaniel H Janzen
Sep 10, 2016·Genome Génome / Conseil National De Recherches Canada·Seikoh SaitohTaizo Nakamori
Oct 5, 2016·Genome Génome / Conseil National De Recherches Canada·Ping-Shin LeeJohn-James Wilson
Oct 21, 2016·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Jedsada SukantamalaJohn-James Wilson
Oct 22, 2016·Genome Génome / Conseil National De Recherches Canada·Joanne E Littlefair, Elizabeth L Clare
Feb 14, 2017·Environmental Science & Technology·Jianghua YangHongxia Yu
Feb 9, 2017·Genome Génome / Conseil National De Recherches Canada·Joanna R Freeland
Sep 25, 2017·International Journal of Molecular Sciences·Pierre FranckJérôme Olivares
Mar 30, 2018·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·John-James WilsonKong-Wah Sing
Oct 2, 2017·Neotropical Entomology·J- D WangR Wang
Feb 20, 2018·Molecular Ecology Resources·Timothy J DivollJoy M O'Keefe
Aug 22, 2018·Molecular Ecology·Carmelo AndújarBrent C Emerson
Sep 19, 2018·Molecular Ecology Resources·Daniel MarquinaFredrik Ronquist
Feb 15, 2018·Bulletin of Entomological Research·G-J Brandon-MongJ-J Wilson
Feb 20, 2019·Molecular Ecology Resources·Thomas W A BraukmannPaul D N Hebert
Nov 8, 2017·Molecular Ecology·Carmelo AndújarAlfried P Vogler
Mar 23, 2017·Biodiversity Data Journal·Matthew L BowserMallory Okuly
Jun 25, 2016·Conservation Biology : the Journal of the Society for Conservation Biology·John-James WilsonAlison K S Wee
Jun 26, 2020·Frontiers in Microbiology·Mariana MateosGeorge Tsiamis
Oct 15, 2019·PeerJ·Vasco ElbrechtDirk Steinke
Dec 4, 2020·Environmental Entomology·Anna F ProbertMargaret C Stanley

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.