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Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform.


ABSTRACT: Genetic 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.

SUBMITTER: Shokralla S 

PROVIDER: S-EPMC4401116 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform.

Shokralla Shadi S   Porter Teresita M TM   Gibson Joel F JF   Dobosz Rafal R   Janzen Daniel H DH   Hallwachs Winnie W   Golding G Brian GB   Hajibabaei Mehrdad M  

Scientific reports 20150417


Genetic 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 marke  ...[more]

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