전복류(Genus Haliotis)의 분류를 위한 단일염기변이 기반 기계학습분석 = Machine Learning SNP for Classification of Korean Abalone Species (Genus Haliotis)

다국어 초록 (Multilingual Abstract)

Climate change is affecting the evolutionary trajectories of individual species and ecological communities, partlythrough the creation of new species groups. As population shift geographically and temporally as a result of climatechange, reproductive interactions between previously isolated species are inevitable and it could potentially lead toinvasion, speciation, or even extinction. Four species of abalone, genus Haliotis are present along the Korean coastlineand these species are important for commercial and fisheries resources management. In this study, genetic markersfor fisheries resources management were discovered based on genomic information, as part of the managementof endemic species in response to climate change. Two thousand one hundred and sixty one single nucleotide polymorphisms(SNPs) were discovered using genotyping-by-sequencing (GBS) method. Forty-one SNPs were selectedbased on their features for species classification. Machine learning analysis using these SNPs makes it possible todifferentiate four Haliotis species and hybrids. In conclusion, the proposed machine learning method has potentialsfor species classification of the genus Haliotis. Our results will provide valuable data for biodiversity conservationand management of abalone population in Korea.

참고문헌 (Reference)

1 이종규, "한국산 전복을 이용한 교잡종 개발" 한국생명과학회 26 (26): 1218-1223, 2016

2 이준상, "한국산 둥근전복속 (고복족상목: 전복과) 의 분류 및 기재" 한국패류학회 30 (30): 79-86, 2014

3 김재원, "한국산 둥근전복, Haliotis discus discus 의 생식주기" 한국패류학회 31 (31): 21-26, 2015

4 박민우, "한국 진도에서 채집된 북방전복, Haliotis discus hannai의 생식주기" 한국패류학회 30 (30): 243-248, 2014

5 동춘매, "종-특이적 PCR 분석법을 이용한 신속하고 간편한 말전복의 종판별법 개발" 한국패류학회 34 (34): 51-59, 2018

6 김혜진, "북방전복(Haliotis discus hannai) 난모세포의 미세구조적 분화" 한국수산과학회 53 (53): 90-97, 2020

7 박철지, "북방전복 (Haliotis discus hannai) 의 mitochondrial DNA 영역별 유전적 변이성 분석" 한국패류학회 29 (29): 335-341, 2013

8 Anthony M. Bolger, "Trimmomatic: a flexible trimmer for Illumina sequence data" Oxford University Press (OUP) 30 (30): 2114-2120, 2014

9 N. H. Barton, "The role of hybridization in evolution" Wiley 10 (10): 551-568, 2001

10 Fred W. Allendorf, "The problems with hybrids: setting conservation guidelines" Elsevier BV 16 (16): 613-622, 2001

11 Martin F. Breed, "The potential of genomics for restoring ecosystems and biodiversity" Springer Science and Business Media LLC 20 (20): 615-628, 2019

12 Adam D. Leaché, "The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics" Annual Reviews 48 (48): 69-84, 2017

13 Ward Appeltans, "The Magnitude of Global Marine Species Diversity" Elsevier BV 22 (22): 2189-2202, 2012

14 Aaron McKenna, "The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data" Cold Spring Harbor Laboratory 20 (20): 1297-1303, 2010

15 Jun Chin Ang, "Supervised, Unsupervised, and Semi-Supervised Feature Selection: A Review on Gene Selection" Institute of Electrical and Electronics Engineers (IEEE) 13 (13): 971-989, 2016

16 강정하, "Possibility of Natural Hybridization between Red Seabream (Pagrus major) and Blackhead Seabream (Acanthopagrus schlegeli)" 한국생명과학회 25 (25): 16-20, 2015

17 M. I. Jordan, "Machine learning: Trends, perspectives, and prospects" American Association for the Advancement of Science (AAAS) 349 (349): 255-260, 2015

18 Tom M. Mitchell, "Machine learning and data mining" Association for Computing Machinery (ACM) 42 (42): 30-36, 1999

19 Siyu Han, "Long Noncoding RNA Identification: Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination" Hindawi Limited 2016 : 1-14, 2016

20 Clint C. Muhlfeld, "Invasive hybridization in a threatened species is accelerated by climate change" Springer Science and Business Media LLC 4 (4): 620-624, 2014

21 Edgar Anderson, "Hybridization of the Habitat" JSTOR 2 (2): 1-9, 1948

22 Amanda J. Chunco, "Hybridization in a warmer world" Wiley 4 (4): 2019-2031, 2014

23 Shawn R. Narum, "Genotyping-by-sequencing in ecological and conservation genomics" Wiley 22 (22): 2841-2847, 2013

24 Armin Scheben, "Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application" Wiley 15 (15): 149-161, 2017

25 John W. Davey, "Genome-wide genetic marker discovery and genotyping using next-generation sequencing" Springer Science and Business Media LLC 12 (12): 499-510, 2011

26 Bo-Hye Nam, "Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae" Oxford University Press (OUP) 6 (6): 1-8, 2017

27 M SCHWARTZ, "Genetic monitoring as a promising tool for conservation and management" Elsevier BV 22 (22): 25-33, 2007

28 JungHa Kang, "Genetic Differentiation of Carassius auratus and C. cuvieri by the Cytochrome C Oxidase I Gene Analysis" OMICS Publishing Group 03 (03): 1-4, 2014

29 Koen Herten, "GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments" Springer Science and Business Media LLC 16 (16): 73-, 2015

30 Ben Langmead, "Fast gapped-read alignment with Bowtie 2" Springer Science and Business Media LLC 9 (9): 357-359, 2012

31 Irawan Asaad, "Ecological criteria to identify areas for biodiversity conservation" Elsevier BV 213 : 309-316, 2017

32 Judith M. Rhymer, "EXTINCTION BY HYBRIDIZATION AND INTROGRESSION" Annual Reviews 27 (27): 83-109, 1996

33 Klemen Čandek, "DNA barcoding gap: reliable species identification over morphological and geographical scales" Wiley 15 (15): 268-277, 2015

34 서용배, "Cytochrome c oxidase subunit 1과 RAPD 분석에 의한 한국 전복속의 계통 연구" 한국생명과학회 26 (26): 406-413, 2016

35 Kemal Murat Canturk, "Current Status of the Use of Single-Nucleotide Polymorphisms in Forensic Practices" Mary Ann Liebert Inc 18 (18): 455-460, 2014

36 Ino T, "Biological studies on the propagation of Japanese abalone(genus Haliotis)" 5 : 1-102, 1953

37 Emma V. A. Sylvester, "Applications of random forest feature selection for fine-scale genetic population assignment" Wiley 11 (11): 153-165, 2018

38 Anna Louise Swan, "Application of Machine Learning to Proteomics Data: Classification and Biomarker Identification in Postgenomics Biology" Mary Ann Liebert Inc 17 (17): 595-610, 2013

39 Humira Sonah, "An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping" Public Library of Science (PLoS) 8 (8): e54603-, 2013

40 X. Zheng, "A high-performance computing toolset for relatedness and principal component analysis of SNP data" Oxford University Press (OUP) 28 (28): 3326-3328, 2012

41 Riley HP, "A character analysis of colonies of Iris fulva, Iris hexagona var. giganticaerulea and natural hybrids" 25 : 727-738, 1938

42 Karl M. Wiegand, "A Taxonomist's Experience with Hybrids in the Wild" American Association for the Advancement of Science (AAAS) 81 (81): 161-166, 1935