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Chemoinformatics-driven classification of Angiosperms using sulfur-containing compounds and machine learning algorithm

Background Phytochemicals or secondary metabolites are low molecular weight organic compounds with little function in plant growth and development. Nevertheless, the metabolite diversity govern not only the phenetics of an organism but may also inform the evolutionary pattern and adaptation of green plants to the changing environment. Plant chemoinformatics analyzes the chemical system of natural products using computational tools and robust mathematical algorithms. It has been a powerful approach for species-level differentiation and is widely employed for species classifications and reinforcement of previous classifications. Results This study attempts to classify Angiosperms using plant sulfur-containing compound (SCC) or sulphated compound information. The SCC dataset of 692 plant species were collected from the comprehensive species-metabolite relationship family (KNApSAck) database. The structural similarity score of metabolite pairs under all possible combinations (plant species-metabolite) were determined and metabolite pairs with a Tanimoto coefficient value > 0.85 were selected for clustering using machine learning algorithm. Metabolite clustering showed association between the similar structural metabolite clusters and metabolite content among the plant species. Phylogenetic tree construction of Angiosperms displayed three major clades, of which, clade 1 and clade 2 represented the eudicots only, and clade 3, a mixture of both eudicots and monocots. The SCC-based construction of Angiosperm phylogeny is a subset of the existing monocot-dicot classification. The majority of eudicots present in clade 1 and 2 were represented by glucosinolate compounds. These clades with SCC may have been a mixture of ancestral species whilst the combinatorial presence of monocot-dicot in clade 3 suggests sulphated-chemical structure diversification in the event of adaptation during evolutionary change. Conclusions Sulphated chemoinformatics informs classification of Angiosperms via machine learning technique. Supplementary Information The online version contains supplementary material available at 10.1186/s13007-022-00951-6.


Background
Angiosperms or flowering plants bearing seeds represent the largest group of living plants. With up to 286000 different species found on land areas, they exist in various forms displaying a wide spectrum of differences in embryology, organ-specific anatomy, micromorphology, palynology and others [1]. Plants produce structurally unique compounds (secondary metabolites) such as the

Open Access
Plant Methods *Correspondence: zeti.hussein@ukm.edu.my polyphenols, alkaloids, terpenes, phenolics, flavonoids and glucosinolates that may or may not significantly support functional roles such as basic processes in growth, development and physiology [2]. The chemical features of natural products are gaining complexity in terms of the content, composition, structure, cellular localization and distribution. The present-day classification of Angiosperms follows morphological characteristics for species-level distinction. There are two major groups in Angiosperms: (i) dicotyledons; seeds with two cotyledons, tap root and leaves with net-like venation and, (ii) monocotyledons; seeds with single cotyledons, adventitious root and leaves with parallel venation. Since plants are bestowed with a broad chemodiversity, these chemical information are harnessed as taxonomy markers in plant natural system classifications [3][4][5]. Nevertheless, no studies have attempted to classify higher taxa plants using chemical information solely as integrative methods are rendered much powerful.
Plant sulfur-containing compounds (SCCs) are S-containing amino acid-derived secondary metabolites [6][7][8]. S is the fourth most essential nutrient to plants after nitrogen, phosphorus and potassium. The S assimilation pathway serves as the precursor for SCC and associated metabolite biosynthesis; methionine, cysteine and phenylalanine amino acids, S-adenosylmethionine coenzyme and glutathione prosthetic groups [9]. In general, SCCs are involved in essential biological activities such as host induced defense responses against microbes and herbivores [10,11], oxidative stress responses and mitigation of heavy-metal toxicity [12]. SCCs display broad chemodiversity which includes glucosinolates, phytosulfokines, sulphated flavonoids and sulfooxy derivatives [13]. In glucosinolates, also the largest group of SCCs, there are about 120 different forms described in higher plants [14]. The SCCs are distributed in numerous species, stretching from grass family (wheat, barley, oat), vegetables (tomato, broccoli, carrot, celery) and fruit trees [15,16].
Chemotaxonomic studies for the classification of plant species have been conducted at various levels with different types of chemical compounds (taxonomic markers), mainly secondary metabolites. For example, species-level differentiation of Hedysarum genus was achieved using chemical profiles of isoflavonoids, chalcones, benzofurans, comestans and pterocarpenes [2], Solanum torvum was distinguishable from its closely related member, S. erianthum using the information from phenolic markers such as delphinidin 3,5-O-diglucoside and malvidin 3-O-arabinoside and 24-methyllathosterol ferulate. Within Selenastraceae, fatty acid methyl ester (FAME)based-chemotaxonomy was successfully used to resolve the uncertainties encountered from using the molecular approach [17]. The significant explosion of metabolomics data and databases coupled with machine learning algorithms inform new knowledge in plant research [18][19][20][21][22][23].
In this study, the graph clustering algorithm (DPClusO) was applied for the identification of overlapping clusters with similar structural SCCs. The DPClusO algorithm generates high density clusters and has been adopted in big data analyses such as protein-protein interactions [24], identification of functional gene relations from gene expression datasets [25], pathway prediction [26] and many others [27]. Chemical information offers important insights into biochemical systematics, however, the scope of SCC chemical structure information to draw organizational concepts in flowering plants is underexplored. Presently, very few studies have attempted to use SCCs as taxonomy markers for plant system classification. Herein, chemoinformatics approach which integrates metabolitecontent and structure similarity information of SCCs are applied for Angiosperms classification.
A total of 4783 metabolite pairs with a Tanimoto coefficient > 0.7 were obtained and 1,200 metabolite pairs with a Tanimoto coefficient > 0.85 were selected for network construction. The structural similarity network consists of 368 SCCs, with 105 single nodes ( Fig. 2A). Single node denotes SCC with non-significant structural similarity score. A total of 335 and 30 SCCs were unique to eudicots and monocots, respectively and three SCCs were present in both eudicot and monocot plants. The degree of network distributions, as determined by power-law elucidated associations between two or more neighbouring nodes [40] (Fig. 2B). Only three SCCs common to eudicot and monocot (purple nodes) showed interactions within the sub-network (Fig. 2). Table 1 shows the metabolite pairs of similar structure SCCs in monocot and eudicot plants. The CoA-containing compounds were present in the following pairs: 1,2 (2-enoyl CoA) and 3 (Acyl CoA). Pair 4 were similar by amino acid grouping whilst pair 5 represented the −OH containing thiosulfinates (dihydroasparagusic acid, asparagusic acid, isobrugierol, brugierol and 3,4-epithiobutyl nitrile). Pair 6, volatile metabolites with an unpleasant odour are sulfide bond containing compounds (hydrogen sulfide, dimethyl disulfide, methyl mercaptan and methyl allyl disulfide). More than half of the metabolite pairs present in both monocot and eudicot plants (pair 7-16) were sulphated flavonoids, a rare representation of flavonoid derivatives (Table 1).

Association between metabolite similarity and biological function
A total of 92 clusters were built with 356 different SCCs; 42 clusters showed association with two or more metabolites (overlapping). The clusters were grouped according to classes of SCCs; glucosinolate, flavonoid, organosulfur, glycoside, phytoalexin, coenzyme, terpenoid, alkaloid, steroid, amino acid and isothiocyanate. Clusters containing glucosinolates showed the highest distribution at 28, followed by clusters of flavonoids (17), organosulfur (11) and glycoside (6) compounds. Clusters with less than five SCCs were comprised of phytoalexin, coenzyme, terpenoid, alkaloid, steroid, amino acid and isothiocyanate compounds (Fig. 3A). Under the network presentation, the flavonoid containing overlapping clusters showed the most number of associations. There were two free networks, each with 10 and 5 overlapping clusters. The network chain with total number of clusters = 10 was mainly represented by monocots. In cluster 12, both the monocot and dicot species were present. The small network chain with 5 overlapping clusters     3B). In the glucosinolate containing overlapping cluster network, only dicot species were identified in all the individual clusters. There were only one big (> 3 clusters) network chain and 3 small chains (≤ 3 clusters). The biggest chain contained 7 individual clusters connected by 13 different glucosinolates. Two chains of three overlapping clusters were connected by 3 and 5 different glucosinolates. There are 4 independent pair-wise clusters connected by a single glucosinolate. Cluster 6 showed the highest number of interactions and appeared as the hub cluster in the glucosinolate overlapping cluster network. Cluster 3-6 were connected by C00007843, C00007586 and C00007857 while cluster 8-6 were connected by C00007340, C00001463, C00001473 and C00007796 (Fig. 3B). In the glycoside and coenzyme network of overlapping clusters, small pairwise networks were observed. The glycoside network of overlapping clusters was represented by monocots only whereas the coenzyme network of overlapping clusters showed a representation of both the eudicots in clusters 27-87 only. In clusters 46-47, monocots were present in cluster 46 only whilst cluster 47 showed a combination of monocots and dicots (Fig. 3B).

Pathway enrichment and Angiosperm phylogeny
From a total of 356 SCCs, only 47 metabolites from 24 clusters were mapped into 53 KEGG metabolic pathways. A total of 23 clusters were involved in the secondary biosynthesis pathway (map01110) whilst 17 clusters showed participation in the 2-oxocarboxylic acid metabolism (map01210) and glucosinolate biosynthesis (map00966). Six clusters were involved in plant secondary metabolite biosynthesis (map01060), and four clusters in cysteine and methionine metabolism (map00270), phenylalanine metabolism (map00360), tryptophan metabolism (map00380), phenylpropanoid biosynthesis (map01061) and plant hormone (map01070) pathways. The SCCs in cluster 1 were involved in flavon and flavonol biosynthesis. The pathway-oriented clustering analysis showed that 23% of SCCs from a similar cluster were mapped within a similar pathway. For example, overlapping clusters composed of clusters 46 and 47 showed the presence of functionally related acetyl-CoA, malonyl-CoA and acetoacetyl-CoA intermediates in lipid, carbohydrate, and amino acid metabolism pathways. The cysteine and methionine metabolism pathway contained clusters 9, 39 and 64 (Fig. 4). In the phenylpropanoid pathway, both clusters 87 and 27 occupied a localized region within the pathway map (Fig. 5).
The pathway-oriented cluster mapping indicated that structurally similar metabolite clusters show localization in reaction steps within the KEGG pathway. Most of the metabolite cluster present in either the intermediary metabolism or specific metabolism of KEGG metabolic pathway maps. In the cysteine and methionine pathway map (map00270), the correlation between cluster 9, cluster 39, and cluster 64 governed the continuous reaction steps. Coumaroyl-CoA found present in cluster 27 and cluster 87 indicate an intermediatory role in the propanoid biosynthesis. In the cysteine and methionine metabolism pathway, three metabolites from cluster 9 and two metabolites each from clusters 39 and 64 were found through the pathway-oriented cluster mapping (Fig. 4). The pathway map is divided into two regions of cysteine pathway (cluster 9) and methionine pathway (cluster 39 and cluster 64). For overlapping clusters, the localized regions of the pathways are highly intercepted between two or more metabolite clusters (Fig. 5). At an average hierarchical clustering value of 50, a total of 46 plant species (92%) represented the eudicot clusters, one (2%) corresponded for monocot cluster and three in monocot-dicot, in combination cluster. Generally, 80% (40) of the clusters, were comprised of eudicots mainly. Among them, 70% of the eudicots were glucosinolate producers. The remaining eudicots from cluster 1, cluster 8, cluster 10, and cluster 44 found in clade 3 showed production of various forms of SCCs (Fig. 6). Similar clusters comprised of both monocot and eudicot plants were found in cluster 1, cluster 5 and cluster 43. In cluster 1, two monocots (Zingiber officinale and Asparagus officinalis) and a single eudicot (Bruguiera gymnorhiza) produced dithiolan and sulfonic acid. Meanwhile, dipropyl disulfide present in Allium sp. (monocot) and Petiveria alliacea (eudicot) were in similar sub-clade under cluster 1. Most of the metabolites from cluster 5 and cluster 43 are composed of SCC from the flavonoid class (Additional file 2). For instance, flavonol O-glycoside, a sulphated flavonoid was highly distributed in eudicot, whereas the flavone C-glycoside or glycoflavone was observed in monocot. Glycoflavone, such as vitalexin, orientin and luteolin were more abundant in monocots as compared to the eudicots [28][29][30][31][32].

Discussion
The sample number poses biasness to a certain extent (eudicot number > monocot number), however, the network clustering performed using DPClusO algorithm corrected for the sampling bias error [33]. Based on Angiosperms chemo-information available in the KNAp-SAck database, a total of 450 different plant species with SCCs was identified. The Angiosperms selected for classification were represented by eudicots, mostly (97% of the total plants). The SCC distribution among the eudicots was much greater as compared to the monocots. Glucosinolate was ranked as the most abundant class of SCC in Angiosperms whereas the isothiocyanate and steroid emerged as the smallest class. From the ecological point of view, glucosinolates are rendered as natural pesticides, posing toxicity to a wide range of organisms from insects, bacteria, fungi, nematodes and mammals [34]. Glucosinolates inherent a chemically stable structure and remain biologically inactive within the sub-cellular compartments distributed within the plant tissues. Glucosinolates are activated by physical actions such as tissue damage, chewing and food processing. The glucosinolate-myrosinase system functions as plant natural defense system against insects and specialized receptor cells stimulated by defoliating pests (eggs and larvae). Upon physical injury, the endogenous enzyme myrosinase hydrolyzes glucosinolate into toxic and antinutritional biologically active products [14]. The glucosinolate representation is inversely proportional to its breakdown products which includes isothiocyanates, oxzzolidine-2-thiones, nitriles, epithionitriles, organic cyanides, oxazolidinethiones and ionic thiocyanate. This explains the association between glucosinolate and the degraded by-products in plant defense system. Flavonoids and organosulfur represented the second most abundant class with up to 98 and 94 SCCs, respectively. With over 5000 chemical structures, the flavonoids display broad diversity and hence, a broad range of functional roles in relation to plant's survival. They impart important roles in numerous plant physiology and ecology-related processes such as seed and flower petal coloration, pollen germination, regulator of plant growth and protection against biotic and abiotic stressors. Metabolites with high similarity scores are likely to be involved in similar biological functions [34,35]. In general, the overlapping clusters obtained in this study displayed a similar metabolite function [36]. Glucosinolate and sulphated flavonoid were distributed in most clusters. In cluster 2, prototribestin (steroid saponin) showed structural similarity with terpenoid-type saponins such as sandrosaponin, tribestin and zygophyloside [49]. In cluster 23, tryptophan derivative compound (3-indolylmethylthiohydroximate) was clustered with indole phytoalexin compounds. Likewise, indole phytoalexin compounds such as cyclobrassinin and indole glucosinolate, sinalbin A and sinalbin B were structurally similar. Metabolites in cluster 29, cluster 30 and cluster 40 were composed of SCCs derived from reaction steps involved in glucosinolate biosynthesis. As such, hexa-, penta-and tetra-homomethionine are Met derivatives involved in the initial step of glucosinolate side-chain elongation while isothiocyanate is the product of the glucosinolate degradation (Table 2).
Structural similarities between the following sulphated flavonoids were observed in cluster 13, cluster 14 and cluster 15: malvidin 3-glucoside-5-(2ʺ-sulfatoglucoside) (C00011343) and orientin 7-O-sulfate (C00006084). Sulphated flavonoids unique to eudicot and monocot were structurally similar (cluster: 12, 13, 14, and 15). In Angiosperms, flavonoids are the most ubiquitously present natural products. Flavonoid sulfation is a conjugation reaction that utilizes sulfate group as donor and flavones, flavonols or their corresponding methyl esters as the acceptor molecules. The sulphated flavonoids are involved in reactive hydroxyl group detoxification, which directly contributes to the hydrophilicity of cellular compartment (solubility). Plants thriving in stressful environment assume sulfate ion sequestration for ecological adaptation. The sulphated flavonoids are naturally present in about 300 plant species comprised of eudicots and monocots [37,38]. The findings corroborated with the present knowledge whereby nearing 50% representation of eudicot-monocot co-occurring metabolite pairs were all sulphated flavonoids. The distribution of SCCs were higher in the eudicots compared to monocots, and so does the structural diversity. The flavonoid containing overlapping clusters showed the most number of associations in the network, implying its broad spectrum functional roles. The interaction between the eudicot and The final product of indole compound degradation monocot sulphated flavonoids suggests structural similarities and/or probable polyphyletic origin among the plant species. Each cluster represents a distinct entity of highly connected structural similarity and thus, may have been involved in similar biological functions [39]. Large clusters are often associated with a broad range of biological functions, in contrast to small clusters that have narrow and specific functions [24,25]. In this study, the pathway-oriented cluster mapping displayed associations between the chemical composition and biochemical pathway. Glucosinolate was uniformly distributed among the Clade 1 eudicots. They were mainly members of the cabbage and mustard family (Brassicaceae), and others listed as the following: Erysimum (highest occurrence), Brassica, Lepidium, Cakile, Thelypodium, Wasabi, Alyssum, Cheiranthus, Malcomia, Eruca, Leavenworthia, Conringia, Iberis, Isatis, DiplotaxisLesquerella, Cardamine and Arabidopsis. Others such as the Gynandropsis from clade 1 represented a higher taxa of the Brassicales order. Members of clade 2 were similar to clade 1 in terms of consistent containment of glucosinolate compound. However, the eudicot members were comprised of several different families listed as the following genera: (i) Brassicaceae; Boechera, Arabis, Lunaria, Christoleaone, Sisymbrium, Thelypodium, Brassica, Crambe, Coincya, Descurainia, Fibigia, Nasturtiopsis, Matthiola, Capsella, Draba, Coincya, Selenia, Peltaria, Rorippa, Raphanus, Schouwia, Diplotaxis, Moricandia, Zilla, Cardamine and others (ii) Tropaeolaceae; Tropaeolum, (iii) Moringaceae; Moringa, (iv) Capparaceae; Capparis, Cleome (uniformly distributed under a single sub-clade), and v) Gyrostemonaceae; Tersonia.

Conclusions
In this study, the chemoinformatics-driven phylogeny of Angiosperms showed parallel results with the traditional morphology-based classification to a great extent. Clade 1 and clade 2 of eudicots were distantly related to clade 3 of eudicot-monocot in combination. Glucosinolate compound was distributed among the species in clade 1-2. Amongst the different classes of SCCs, glucosinolate was ranked as the most abundant class whereas the isothiocyanate and steroid emerged as the smallest class. The flavonoids emerged as the second most abundant class after glucosinolate. Both glucosinolate and flavonoids have shown apparent structural diversity implicated in the trajectory of plant evolution driving the species chemodiversity. The first is important in plant defense response, adaptability, tolerance against stressors and cellular level physiobiochemical activities, whereas, the latter plays a fundamental role in growth and development, and physiological processes.

Data collection and pre-processing
Plant-specific sulfur-containing compounds (SCCs) were collected from KNApSAck Core DB and KNApSAck DB (https:// www. knaps ackfa mily. com/ knaps ack). A total of 552 SCCs were identified from 692 plant species. Plants with less than two different SCCs were manually filtered out from the dataset. The corresponding.MOL files for all the identified metabolites were retrieved from the KNApSAcK Core DB. The SCCs were annotated via bibliomic search using the following databases: PubChem (https:// www. pubch em. ncbi. nlm. nih. gov) [40], KEGG (https:// www. genome. jp/) [41,42] and Metlin (https:// www. scrip ps. edu) [43]. Figure 7 illustrates the schematic workflow of the method employed in this study.

Structural similarity analysis
The structural similarities of the identified SCCs were determined using the ChemmineR, an R-package, version 2.30.2 [44]. The atom pair fingerprints of all SCCs were generated from the.MOL metabolite structure input files and the structural similarities between pairs of metabolites were determined by Tanimoto coefficient. The Tanimoto coefficient values range from 0-1 (with increased value, the stronger the structural similarity), whereby 0 denotes no structural similarity and 1 indicates the highest similarity. The Tanimoto coefficient cut-off value was set at > 0.85 [45,46]. All metabolite pairs were screened by Tanimoto coefficient and pairs that did not meet the cut-off value were filtered out from the metabolic network construction input data [47]. The metabolite network was visualized using Cytoscape software, version 3.6.1 [48].

Sulfur-containing compound (SCC) cluster
DPClusO graph clustering algorithm was used for the identification of overlapping clusters from the metabolite network comprised of structurally similar SCCs pairs [49]. The parameters deployed in the algorithm for the cluster k are defined as follows: (i) cluster property ( cp nk ), (ii) density ( d k ), (iii) ratio of the edges (|E k |) and, (iv) maximum possible number of edges(|E k |max) . The d k was calculated using |E k |) and |E k |max . N k represents the number of nodes in cluster k. The E nk denotes the total number of edges between the node, n and the cluster nodes [40]. The cluster property(cp nk ) of node (n) in cluster k is shown below: cp nk = |E nk | d k x|N k | Author contributions MZ designed and performed the research, analyzed the data and drafted the manuscript, NG validated the output, and revised the manuscript, MBK, MA, SK analyzed the data, provided the computing resources, technical assistance and coordinated the analyses. ZM conceived the study, coordinated the research flow, revised the draft manuscript, provided supervision and secured funding. All authors read and approved the final manuscript.

Availability of data and materials
The chemoinfomatics data sets utilized in this study are available at https:// www. knaps ackfa mily. com/ knaps ack.