Decision Theory-Based COI-SNP Tagging Approach for 126 Scombriformes Species Tagging

Cheng-Hong Yang; Kuo-Chuan Wu; Li-Yeh Chuang; Hsueh-Wei Chang

doi:10.3389/fgene.2019.00259

Decision Theory-Based COI-SNP Tagging Approach for 126 Scombriformes Species Tagging

Front Genet. 2019 Apr 3:10:259. doi: 10.3389/fgene.2019.00259. eCollection 2019.

Authors

Cheng-Hong Yang^{1

2}, Kuo-Chuan Wu^{1

3}, Li-Yeh Chuang⁴, Hsueh-Wei Chang^{5

6

7}

Affiliations

¹ Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan.
² Biomedical Engineering, Kaohsiung Medical University, Kaohsiung, Taiwan.
³ Department of Computer Science and Information Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan.
⁴ Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.
⁵ Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan.
⁶ Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
⁷ Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.

Abstract

The mitochondrial gene cytochrome c oxidase I (COI) is commonly used for DNA barcoding in animals. However, most of the COI barcode nucleotides are conserved and sequences longer than about 650 base pairs increase the computational burden for species identification. To solve this problem, we propose a decision theory-based COI SNP tagging (DCST) approach that focuses on the discrimination of species using single nucleotide polymorphisms (SNPs) as the variable nucleotides of the sequences of a group of species. Using the example of 126 teleost mackerel fish species (order: Scombriformes), we identified 281 SNPs by alignment and trimming of their COI sequences. After decision rule making, 49 SNPs in 126 fish species were determined using the scoring system of the DCST approach. These COI-SNP barcodes were finally transformed into one-dimensional barcode images. Our proposed DCST approach simplifies the computational complexity and identifies the most effective and fewest SNPs to resolve or discriminate species for species tagging.

Keywords: COI; DCST; barcoding; decision theory; single nucleotide polymorphism (SNP); species identification; teleost fish.