Yang Cheng-Hong, Wu Kuo-Chuan, Dahms Hans-Uwe, Chuang Li-Yeh, Chang Hsueh-Wei
Department of Electronic Engineering National Kaohsiung University of Applied Sciences Kaohsiung Taiwan.
Graduate Institute of Clinical Medicine Kaohsiung Medical University Kaohsiung Taiwan.
Ecol Evol. 2017 May 23;7(13):4717-4725. doi: 10.1002/ece3.3045. eCollection 2017 Jul.
DNA barcodes are widely used in taxonomy, systematics, species identification, food safety, and forensic science. Most of the conventional DNA barcode sequences contain the whole information of a given barcoding gene. Most of the sequence information does not vary and is uninformative for a given group of taxa within a monophylum. We suggest here a method that reduces the amount of noninformative nucleotides in a given barcoding sequence of a major taxon, like the prokaryotes, or eukaryotic animals, plants, or fungi. The actual differences in genetic sequences, called single nucleotide polymorphism (SNP) genotyping, provide a tool for developing a rapid, reliable, and high-throughput assay for the discrimination between known species. Here, we investigated SNPs as robust markers of genetic variation for identifying different pigeon species based on available cytochrome c oxidase I (COI) data. We propose here a decision tree-based SNP barcoding (DTSB) algorithm where SNP patterns are selected from the DNA barcoding sequence of several evolutionarily related species in order to identify a single species with pigeons as an example. This approach can make use of any established barcoding system. We here firstly used as an example the mitochondrial gene COI information of 17 pigeon species (Columbidae, Aves) using DTSB after sequence trimming and alignment. SNPs were chosen which followed the rule of decision tree and species-specific SNP barcodes. The shortest barcode of about 11 bp was then generated for discriminating 17 pigeon species using the DTSB method. This method provides a sequence alignment and tree decision approach to parsimoniously assign a unique and shortest SNP barcode for any known species of a chosen monophyletic taxon where a barcoding sequence is available.
DNA条形码广泛应用于分类学、系统学、物种鉴定、食品安全和法医学领域。大多数传统的DNA条形码序列包含特定条形码基因的全部信息。对于一个单系类群中的特定分类单元组而言，大部分序列信息并无变化且不具有信息价值。我们在此提出一种方法，可减少主要分类单元（如原核生物、真核动物、植物或真菌）特定条形码序列中无信息核苷酸的数量。遗传序列中的实际差异，即单核苷酸多态性（SNP）基因分型，为开发一种快速、可靠且高通量的方法以区分已知物种提供了工具。在此，我们基于现有的细胞色素c氧化酶I（COI）数据，研究了SNP作为遗传变异的可靠标记以识别不同鸽类物种。我们在此提出一种基于决策树的SNP条形码（DTSB）算法，从几个进化相关物种的DNA条形码序列中选择SNP模式，以鸽类为例识别单一物种。这种方法可利用任何已建立的条形码系统。我们首先以17种鸽类（鸽科，鸟类）的线粒体基因COI信息为例，在序列修剪和比对后使用DTSB方法。选择遵循决策树规则和物种特异性SNP条形码的SNP。然后使用DTSB方法生成约11bp的最短条形码以区分17种鸽类物种。该方法提供了一种序列比对和树状决策方法，用于为任何具有条形码序列的选定单系分类单元的已知物种简洁地分配唯一且最短的SNP条形码。
