Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform Journal Articles uri icon

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  • AbstractGenetic information is a valuable component of biosystematics, especially specimen identification through the use of species-specific DNA barcodes. Although many genomics applications have shifted to High-Throughput Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample identification (e.g., via DNA barcoding) is still most often done with Sanger sequencing. Here, we present a scalable double dual-indexing approach using an Illumina Miseq platform to sequence DNA barcode markers. We achieved 97.3% success by using half of an Illumina Miseq flowcell to obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010 specimens from eleven orders of arthropods. Our approach recovers a greater proportion of DNA barcode sequences from individuals than does conventional Sanger sequencing, while at the same time reducing both per specimen costs and labor time by nearly 80%. In addition, the use of HTS allows the recovery of multiple sequences per specimen, for deeper analysis of genetic variation in target gene regions.


  • Shokralla, Shadi
  • Porter, Teresita M
  • Gibson, Joel F
  • Dobosz, Rafal
  • Janzen, Daniel H
  • Hallwachs, Winnie
  • Golding, Brian
  • Hajibabaei, Mehrdad

publication date

  • April 17, 2015