title: UPLC-QTOFMS based metabolomics followed by stepwise partial least square-discriminant analysis (PLS-DA) explore the possible relation between the variations in secondary metabolites and the phylogenetic divergences of the genus Panax.
abstract: Phylogenetic and metabolomic approaches have long been employed to study evolutionary relationships among plants. Nonetheless, few studies have examined the difference in metabolites within a clade and between clades of the phylogenetic tree. We attempted to relate phylogenetic studies to metabolomics using stepwise partial least squares-discriminant analysis (PLS-DA) for the genus Panax. Samples were analyzed by ultra-performance liquid chromatography-quadrupole time of flight mass spectrometry (UPLC-QTOFMS) to obtain metabolite profiles. Initially, conventional principal component analysis was subsequently applied to the metabolomic data to show the limitations in relating the expression of metabolites to divisions in the phylogenetic tree. Thereafter, we introduced stepwise PLS-DA with optimized scaling methods, which were properly applied according to the branches of the phylogenetic tree of the four species. Our approach highlighted metabolites of interest by elucidating the directions and degrees of metabolic alterations in each clade of the phylogenetic tree. The results revealed the relationship between metabolic changes in the genus Panax and its species' evolutionary adaptations to different climates. We believe our method will be useful to help understand the metabolite-evolution relationship.
authors.affiliation: College of Pharmacy, Seoul National University, Seoul 08826, South Korea.
authors.forename: Huy Truong
authors.initials: HT
authors.lastname: Nguyen
authors.affiliation: College of Pharmacy, Seoul National University, Seoul 08826, South Korea.
authors.forename: Dong-Kyu
authors.initials: DK
authors.lastname: Lee
authors.affiliation: College of Pharmacy, Seoul National University, Seoul 08826, South Korea.
authors.forename: Won Jun
authors.initials: WJ
authors.lastname: Lee
authors.affiliation: College of Pharmacy, Seoul National University, Seoul 08826, South Korea.
authors.forename: GwangJin
authors.initials: G
authors.lastname: Lee
authors.affiliation: College of Pharmacy, Seoul National University, Seoul 08826, South Korea.
authors.forename: Sang Jun
authors.initials: SJ
authors.lastname: Yoon
authors.affiliation: College of Pharmacy, Seoul National University, Seoul 08826, South Korea.
authors.forename: Byong-Kyu
authors.initials: BK
authors.lastname: Shin
authors.affiliation: Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
authors.forename: Minh Duc
authors.initials: MD
authors.lastname: Nguyen
authors.affiliation: Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam; College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, South Korea; Institute of Green Bio Science Technology, Seoul National University, Pyeongchang, Gangwondo 25354, South Korea.
authors.forename: Jeong Hill
authors.initials: JH
authors.lastname: Park
authors.affiliation: School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea. Electronic address: jlee0610@skku.edu.
authors.forename: Jeongmi
authors.initials: J
authors.lastname: Lee
authors.affiliation: College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, South Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, South Korea. Electronic address: swkwon@snu.ac.kr.
authors.forename: Sung Won
authors.initials: SW
authors.lastname: Kwon
mesh_terms: D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics; D016002:Discriminant Analysis; D016018:Least-Squares Analysis; D013058:Mass Spectrometry / Q000379:methods*; D055432:Metabolomics / Q000379:methods*; D005894:Panax / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny
chemical_list: D018744:DNA, Plant
keywords: Genus Panax; Metabolomics; Phylogenetic mapping; Secondary metabolites; Stepwise partial least square-discriminant analysis