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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Maxam-Gilbert Sequencing01:05

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In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
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Sanger Sequencing01:57

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications
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Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications

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

Shanlin Liu1,2,3, Chentao Yang2, Chengran Zhou1,4

  • 1Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing 100193, People's Republic of China.

Gigascience
|October 28, 2017
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Summary
This summary is machine-generated.

We developed HIFI-Barcode, an affordable DNA barcoding pipeline using Illumina sequencing. This method accurately identifies species and significantly reduces costs for global biodiversity research.

Keywords:
BiodiveristyCOIDNA BarcodeHigh-throughput sequencingmeta-barcoding

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Area of Science:

  • Genomics
  • Biodiversity Science
  • Molecular Biology

Background:

  • DNA barcoding is crucial for species identification but faces cost limitations with traditional Sanger sequencing.
  • Current DNA barcoding costs hinder global efforts and the application of high-throughput sequencing (HTS) for taxonomic identification.
  • Existing methods struggle to link HTS data to binomial species names, limiting biological knowledge integration.

Purpose of the Study:

  • To develop a cost-effective, high-throughput DNA barcoding pipeline for generating full-length Cytochrome c oxidase subunit I (COI) barcodes.
  • To enable accurate species identification and facilitate the creation of comprehensive barcode libraries for global biodiversity assessment.
  • To overcome the cost and throughput limitations of Sanger sequencing for DNA barcoding.

Main Methods:

  • Developed the HIFI-Barcode pipeline utilizing Illumina sequencing technology for pooled polymerase chain reaction (PCR) amplicons from individual specimens.
  • Generated full-length COI barcodes, ensuring accuracy comparable to Sanger sequencing standards, even for closely related haplotypes.
  • Validated HIFI-Barcode accuracy using Pacbio single molecular sequencing and assessed its sensitivity in recovering low-quantity amplicons.

Main Results:

  • The HIFI-Barcode pipeline produces accurate, full-length COI barcodes comparable to Sanger sequencing standards.
  • Demonstrated high sensitivity, successfully recovering barcodes from over 78% of PCRs with no visible bands on electrophoresis gels.
  • Achieved significant cost reduction, estimating the new pipeline at approximately one-tenth the cost of current methods.

Conclusions:

  • The HIFI-Barcode pipeline offers a substantial advancement in DNA barcoding technology, significantly reducing costs and increasing throughput.
  • This method enables the construction of comprehensive barcode libraries, crucial for advancing local and global biodiversity research.
  • Provides a feasible pathway for widespread DNA barcoding of global biomes, enhancing species identification and taxonomic efforts.