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Efficient COI barcoding using high throughput single-end 400 bp sequencing.

Chentao Yang1, Yuxuan Zheng2, Shangjin Tan1

  • 1BGI-Shenzhen, Shenzhen, 518083, China.

BMC Genomics
|December 5, 2020
PubMed
Summary
This summary is machine-generated.

A new HIFI-SE pipeline efficiently assembles full-length DNA barcodes from pooled sequencing data. This method overcomes read length limitations and high costs, advancing DNA-based species identification.

Keywords:
BiodiversityCOIDNA barcodeHigh-throughput sequencingMGISEQ-2000SE400

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • High-throughput sequencing accelerates species description via DNA barcoding.
  • Current methods face limitations in read length, cost, and output for full-length barcodes.

Purpose of the Study:

  • To develop a bioinformatic pipeline (HIFI-SE) for assembling full-length DNA barcodes from pooled sequencing data.
  • To overcome limitations of existing high-throughput DNA barcoding techniques.

Main Methods:

  • Sequencing pooled cytochrome c oxidase subunit I (COI) barcodes on the MGISEQ-2000 platform (SE400).
  • Utilizing the HIFI-SE Python pipeline with filter, assign, assembly, and taxonomy modules.
  • Assembling reads from 5' and 3' ends of the COI barcode region.

Main Results:

  • Successfully assembled 747 full-length COI barcodes from 845 samples (marine invertebrates and insects).
  • Identified 70 Wolbachia and fungi symbionts.
  • Achieved high accuracy in assembly compared to Sanger sequences (71/72 samples correctly assembled).

Conclusions:

  • The HIFI-SE pipeline offers an efficient, cost-effective, and sensitive method for producing standard full-length barcodes.
  • This approach enhances DNA-based species identification across diverse ecosystems.
  • Increases the volume of DNA barcodes generated within budget constraints.