Experimental quantification of pollen with DNA metabarcoding using ITS1 and trnL.

Scientific Reports
Sandra BaksayNathalie Escaravage

Abstract

Although the use of metabarcoding to identify taxa in DNA mixtures is widely approved, its reliability in quantifying taxon abundance is still the subject of debate. In this study we investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high-throughput sequence reads and how the relationship was affected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have different characteristics. We found a significant positive relationship between the number of DNA sequences and the number of pollen grains in the mock solutions. However, better relationships were obtained with light microscopy as a pollen grain counting method compared with flow cytometry, with the chloroplastic trnL marker compared with ribosomal ITS1 and with 30 when compared with 25 or 35 PCR cycles. We provide a list of recommendations to improve pollen quantification.

References

Nov 10, 2000·Biochimica Et Biophysica Acta·P Kainz
Sep 2, 2008·Computational Biology and Chemistry·T G MamedovH J Viljoen
Apr 11, 2012·Molecular Ecology·Pierre TaberletLoren H Rieseberg
Jan 9, 2014·Environmental Toxicology and Chemistry·Anthony A CharitonRobin A Matthews
Feb 8, 2014·BioTechniques·Steven R HeadPhillip Ordoukhanian
May 14, 2014·Trends in Ecology & Evolution·Kristine BohmannMark de Bruyn
Oct 9, 2014·PloS One·Andrea GalimbertiMassimo Labra
Jan 22, 2015·Applications in Plant Sciences·Rodney T RichardsonReed M Johnson
May 12, 2015·Molecular Ecology Resources·Frédéric BoyerEric Coissac
Jun 3, 2015·Molecular Ecology Resources·Nathan T EvansDavid M Lodge
Dec 10, 2015·Applications in Plant Sciences·Rodney T RichardsonReed M Johnson
Jun 4, 2016·Scientific Reports·André PornonChristophe Andalo
Sep 10, 2016·Genome Génome / Conseil National De Recherches Canada·Seikoh SaitohTaizo Nakamori
Mar 9, 2017·PloS One·Rashmi Prava MohantyEstelle Levetin
Mar 25, 2017·Applications in Plant Sciences·Karen L BellBerry J Brosi
Jul 12, 2017·Applications in Plant Sciences·Karen L BellBerry J Brosi
Sep 19, 2017·Molecular Ecology·Kristy DeinerLouis Bernatchez
Dec 6, 2017·Scientific Reports·André PornonNathalie Escaravage
Feb 1, 2018·Genome Biology and Evolution·Marie-Ka TilakBenoit Nabholz
Nov 9, 2018·Molecular Ecology·Philip D LambMartin I Taylor
Jul 22, 2019·Molecular Ecology Resources·Dandan LangXin Zhou

❮ Previous
Next ❯

Citations

Mar 25, 2021·Scientific Reports·Juan LobatonRomina Rader
Apr 7, 2021·Journal of Economic Entomology·Alina AvanesyanWilliam O Lamp
Apr 14, 2021·Environmental Research·Chiara SuannoStefano Del Duca
Jul 15, 2021·Ecology and Evolution·Liz MillaFrancisco Encinas-Viso
Aug 12, 2021·Scientific Reports·Chelsea LennartzJames Comolli

❮ Previous
Next ❯

Methods Mentioned

BETA
light microscopy
PCR
flow cytometry
light
flow

Software Mentioned

obiuniq
OBITOOL
obiclean
Illumina
R package
ecoTag

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.