DOI: 10.5061/dryad.ps8ng8g
title: Data from: Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding

description: 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 library that
 includes 78 families and 96 genera from all major plant lineages,
 including bryophytes, ferns and lycophytes, gymnosperms, and all major
 groups of angiosperms, which are currently lacking in public databases.
 Our results demonstrate that this technique offers a highly efficient
 alternative method to traditional PCR and Sanger sequencing by increasing
 the estimated number of plant DNA barcodes that can be sequenced by a
 single technician in one week by 800%, at a reduced cost, and by
 generating a barcode library with a more comprehensive taxonomic coverage.
description: 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 contains the scripts for creating bwa reference indices and to subsequently process the assembly of reads to these indices. BWA_Indices_and_AssemblyScripts All Reference Sequences for bwa assembly This file contains all .fasta formatted sequence data for each reference used for bwa assemblies in this study. The name for each reference assembly .fasta is provided in the #commented portion above each .fasta block. The reference names match the name of the reference .fasta called in the bwa index script. All_RefsForbwaIndices.fasta QIIME2_CommandsUsedForAnalysis This is a .txt file that contains the entire set of QIIME2 commands used for sequence read processing and analysis in our assessment of the performance of MEBarcoding.