Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding
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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 Junoâ¢, 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..., ,
DNA条形码（DNA barcoding）已成为支撑物种鉴定的宝贵工具，在传统分类学、生态学、法医学、食品分析及环境科学等领域拥有广泛应用。本研究推出面向植物DNA条形码的微流控富集条形码技术（Microfluidics Enrichment Barcoding，简称MEBarcoding），这是一种可实现高通量DNA条形码测序的低成本方法。 MEBarcoding采用Fluidigm Access Array™系统，可在单次热循环程序中同时对48个DNA样本及数百对PCR引物的靶向区域进行扩增，总计可生成23040个PCR产物。Fluidigm推出的第二代仪器Juno™可同时处理192个DNA样本。 作为概念验证，我们依托Fluidigm Access Array™与Illumina MiSeq搭建了一套微流控PCR工作流程，从96个植物样本中分别获取四大核心植物DNA条形码位点的新序列：rbcL、matK、trnH-psbA及ITS，总计384条序列。该工作流程被用于构建参考文库…… Fasta_File_Containing_ITS_Sequences 本文件为FASTA格式，包含本研究通过MEBarcoding方法获得的全部ITS序列，对应文件名为ITS.fasta。 Fasta_File_Containing_matK_Sequences 本文件为FASTA格式，包含本研究通过MEBarcoding方法获得的全部matK序列，对应文件名为matK.fasta。 Fasta_File_Containing_psbA-trnH_Sequences 本文件为FASTA格式，包含本研究通过MEBarcoding方法获得的全部psbA-trnH序列，对应文件名为psbAtrnH.fasta。 Fasta_File_Containing_rbcL_Sequences 本文件为FASTA格式，包含本研究通过MEBarcoding方法获得的全部rbcL序列，对应文件名为rbcL.fasta。 CutAdaptScript_MicroBarcodes 本文件包含本研究中使用Cutadapt程序对MiSeq原始测序reads进行接头修剪的脚本。 Samtools script for this study 本文件包含用于将BWA生成的.sam文件转换为.bam格式的Samtools脚本，对应文件名为Samtools_Script。 BWA Reference Index and Assembly Script 本文件……
