Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding

DNA barcoding has become a valuable tool to support species identification with a broad range of applications in fields such as traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidics Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array™ to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (a total of 23,040 PCR products) during a single thermal cycling protocol. A second generation instrument from Fluidigm, called the Juno™, can accommodate 192 DNA samples simultaneously. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array™ and Illumina MiSeq to generate new sequences from 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS (384 total sequences). This workflow was used to build a reference libr...,
Fasta_File_Containing_ITS_Sequences
This is a .fasta file containing all ITS sequences produced by this study using the MEBarcoding approach.
ITS.fasta

Fasta_File_Containing_matK_Sequences
This is a .fasta file containing all matK sequences produced in this study using the MEBarcoding approach.
matK.fasta

Fasta_File_Containing_psbA-trnH_Sequences
This is a .fasta file containing all psbA-trnH sequences produced in this study using the MEBarcoding approach.
psbAtrnH.fasta

Fasta_File_Containing_rbcL_Sequences
This is a .fasta file containing all rbcL sequences produced in this study using the MEBarcoding approach.
rbcL.fasta

CutAdaptScript_MicroBarcodes
This file contains the script used to trim and cut adapters from raw MiSeq reads produced in this study using the program Cutadapt.
 

Samtools script for this study
This file contains the Samtools script used to convert .sam files produced by BWA to .bam format.
Samtools_Script

BWA Reference Index and Assembly Script
This file..., ,