Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world

GigaScience
Shanlin LiuXin Zhou

Abstract

Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)-based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered bar...Continue Reading

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Citations

May 18, 2018·Immunology·Muzamil Y WantKunle Odunsi
Jul 22, 2019·Molecular Ecology Resources·Dandan LangXin Zhou
Jun 17, 2020·Molecular Ecology·Kristine BohmannM Thomas P Gilbert
Apr 13, 2020·Molecular Ecology Resources·Alejandra OrtegaCarlos M Duarte
Jun 17, 2021·Applied and Environmental Microbiology·Leho TedersooBenjamin Callahan
Aug 10, 2021·Marine Pollution Bulletin·Vignesh Kumar BalasubramanianRamesh Ramachandran

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Datasets Mentioned

BETA
PRJNA414137

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

VSEARCH
iTOL
COAP
BWA
house Perl scripts
io
MEGA7
Hiseq
Pacbio
Barcode

Related Concepts

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Biodiversity Data

Biodiversity refers to the variety and variability of life on Earth. Biodiversity is typically a measure of variation at the genetic, species, and ecosystem level.Discover the latest research on biodiversity data here.

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