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Supplementary Materials for 4 5 Did a Plant-Herbivore Arms Race Drive Chemical Diversity in Euphorbia? 6 7 M

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Supplementary Materials for 4 5 Did a Plant-Herbivore Arms Race Drive Chemical Diversity in Euphorbia? 6 7 M 1 2 3 Supplementary Materials for 4 5 Did a plant-herbivore arms race drive chemical diversity in Euphorbia? 6 7 M. Ernst1,2,3, L.-F. Nothias2,3, J. J. J. van der Hooft2,3,4, R. R. Silva2,3, C. H. Saslis-Lagoudakis1, 8 O. M. Grace5, K. Martinez-Swatson1, G. Hassemer1, L. A. Funez7, H. T. Simonsen6, M. H. 9 Medema4, D. Staerk8, N. Nilsson9, P. Lovato9, P. C. Dorrestein2,3,10∗ & N. Rønsted1∗ 10 11 *Correspondence to: [email protected] and [email protected] 12 13 14 This PDF file includes: 15 16 Materials and Methods 17 Supplementary Text 18 Table S1 19 Fig S1-S12 20 URL S1 21 Captions for Data S1 and S2 22 23 Other Supplementary Materials for this manuscript include the following: 24 25 Data S1 and S2 26 27 ● List of Euphorbia species sampled. 28 ● High-resolution TNF-α modulation profiles. 29 1 30 Materials and Methods 31 32 Collection of plant material 33 34 Pooled extracts of specimens for each Euphorbia species 35 36 43 Euphorbia species (Data S1) were collected from the greenhouses of the Living Collections 37 of the Botanical Garden in Copenhagen. Live plants were sampled for xerophytic species, 38 whereas herbaceous perennials were grown from seeds originating from the seed bank of the 39 Botanical Garden or collections performed in southern Brazil (Species 11-14 and 16-18). E. 40 myrsinites and E. amygdaloides were purchased as live plants from Jespers Planteskole, 41 Holstebro A/S, Harrestrupvej 64, 7500 Holstebro and Kridtvejs Planter, Kridtvej 18, 7980 42 Vils, Denmark and kept in the greenhouse with the other herbaceous species until harvest. To 43 get representative samples of the specialized metabolite profile in the living plants, the plants 44 were sampled as whole intact specimens with the roots included. Over six specimens or as 45 many available from the collections were sampled for each species (Data S1). Some tree 46 species or rare species could not be sampled as whole plants, in these cases, branches of 47 representative parts of the living specimen were sampled (Data S1). The fresh plant material 48 was then stored at -20◦C until extract preparation. Voucher specimens were prepared for 49 species with enough material available from the Living Collections and deposited at the 50 General herbarium of vascular plants, Natural History Museum of Denmark, Copenhagen. 51 Taxonomic species identity was confirmed for all species sampled based on the voucher 52 specimens, the living specimens in the greenhouse or photographs. 53 54 3D mass spectral molecular cartography 55 56 Individual plant parts from one to three specimens of one representative species of each 57 subgeneric clade of Euphorbia were sampled (E. horrida, Athymalus, 3 specimens; E. hirta, 58 Chamaesyce, 2 specimens; E. lathyris, Esula, 2 specimens; E. milii, Euphorbia, 2 specimens). 59 Approximately 200 mg fresh plant material of each individual plant part was collected in 1.5 60 ml Eppendorf tubes and flash frozen under liquid nitrogen. The samples were stored at -80◦C 61 until further analysis. 62 63 Extract preparation 64 65 Pooled extracts of specimens for each Euphorbia species 66 67 Individual specimens of the same species were pooled, and the frozen plant material was 68 disrupted with a pestle and mortar in liquid nitrogen and app. 75 g was extracted with 975 ml 69 ethyl acetate (VWR Chemicals, HiPerSolv Chromanorm) under sonication (Fisher Scientific) 70 at 40◦C during 2 h. The extracts were filtered and evaporated to dryness on a rotary evaporator. 71 The dried extracts were then resuspended in acetonitrile (VWR Chemicals, HiPerSolv 72 Chromanorm), extracted under sonication (Fisher Scientific) at 40◦C during 15 min, filtered 73 and evaporated to dryness. 2 74 75 3D mass spectral molecular cartography 76 77 The frozen plant material was disrupted in plastic tubes (Qiagen, RB 2 mL) in 1.3 ml 50/50 78 vol/vol methanol (Fisher Scientific, HPLC Grade)/acetonitrile (Fisher Scientific, Optima 79 LC/MS) with stainless steel beads (VWR International, 5 mm) using a tissue lyser (Qiagen, 80 TissueLyser II) at 25 Hz during 10 min. The samples were then extracted under sonication 81 (Fisher Scientific) at 40◦C during 15 min and centrifuged (Eppendorf Centrifuge 5418) for 10 82 min at 11,000 r.p.m. The extract supernatant was transferred to new plastic tubes and 83 lyophilized to dryness (Labcono, Acid Resistant CentriVap Concentrator). 84 85 LC-MS/MS analysis 86 87 Pooled extracts of specimens for each Euphorbia species 88 89 Extracts were transferred to a 96-well plate (Falcon, 96-well plates, 0.34 ml, polypropylene) 90 and dried with a vacuum centrifuge. Samples were redissolved in 3/7 vol/vol methanol (Fisher 91 Scientific, HPLC Grade)/acetonitrile (Fisher Scientific, Optima LC/MS) to a concentration of 92 10 mg/ml, in a volume of 150 µL, with a 100 mM concentration of ammonium formate, 93 sealed with Zone-Free Sealing Film (Excel Scientific) and centrifuged for 30 min. at 2000 94 r.p.m. at 4◦C. Ammonium formate was used to promote the ionisation of diterpene esters as 95 ammonium adducts rather than sodiated adducts, thus inducing a richer MS/MS fragmentation 96 pattern as described by Vogg and collaborators (31). MS analysis was performed on a qTOF 97 Maxis II (Bruker Daltonics) mass spectrometer with an electrospray ionization (ESI) source, 98 controlled by OTOF control and Hystar. Each sample was analyzed separately two times with 99 two different MS-methods for MS acquisition. For the first MS-method, 5 µL were injected, 100 auto-MS/MS was turned off, whereas for the second MS-method, 20 µL were injected and 101 auto-MS/MS was activated. For both MS-methods, MS spectra were acquired in positive ion 102 mode over a mass range of 75-1,000 m/z. An external calibration with sodium formate was 103 performed before data acquisition and hexakis(1H,1H,3H- tetrafluoropropoxy)phosphazene 104 (Synquest Laboratories) m/z 922.009798 was used as a lock mass internal calibrant during 105 data acquisition. The following instrument settings were used for data acquisition: end plate 106 Offset 500 V, capillary voltage of 5,000 V, nebulizer gas (nitrogen) pressure of 2.0 bar, ion 107 source temperature of 200◦C, dry gas flow of 9 l min−1, source temperature and spectra 108 acquisition rate of 4 Hz for MS1 and MS2. Tune parameters were set as follows: Funnel RF1 109 200 Vpp, ion energy 3.0 V, Hexapole RF 80 Vpp, Pre pulse storage 7 µs. Minutes 0-0.7 were 110 sent to waste. For the MS-method with auto-MS/MS turned on, the three most intense ions per 111 MS1 scan were selected and subjected to collision-induced dissociation if absolute intensity 112 reached 12205 counts. The following fragmentation and isolation lists were used (values are 113 m/z, isolation width and collision energy, respectively): 100, 2, 10; 250, 2, 15; 300, 2, 20; 400, 114 2, 20; 500, 2, 20; 600, 2, 30; 700, 2, 30; 800, 2, 30; 1000, 2, 40. In addition, the advanced 115 stepping function was used with time, collision radiofrequency (RF), transfer time stepping 116 (µs) and collision energy set to: 0, 800, 85, 75; 400, 65, 100, 100; 50, 400, 65, 100; 75, 150, 117 45, 150. The MS/MS active exclusion parameter was set to 1 and released after 0.25 min, and 118 reseted if ion intensity was three times higher. The injected samples were chromatographically 119 separated using an Agilent 1290 Infinity Binary LC System (Agilent Technologies) controlled 3 120 by Hystar software (Bruker Daltonics), using a 100 x 2.1 mm Kinetex 1.7 µM, C18, 100 Å 121 chromatography column (Phenomenex), 40◦C column temperature, 0.5 ml min−1 flow rate, 122 mobile phase A 99.9% water (Fisher Scientific, Optima LC/MS)/0.1% formic acid (Fisher 123 Scientific, Optima LC/MS)/10 mM ammonium formate (Fluka, LC-MS Ultra), mobile phase B 124 99.9% acetonitrile (Fisher Scientific, Optima LC/MS)/0.1% formic acid (Fisher Scientific, 125 Optima LC/MS)/10 mM ammonium formate (Fluka, LC-MS Ultra), with the following 126 gradient: 0-0.5 min 55% B, 0.5-15 min 100% B, 15-18.5 min 100% B, 18.5-20 min 100% B. 127 Blanks were injected between each analyzed sample, and the column was equilibrated prior to 128 any injection with the following gradient 20-20.2 min 55% B, 20.2-20.4 min 100% B, 20.4-23 129 min 55% B, 23-25 min 55%. Blank injections - 20 µL methanol:acetonitrile (3:7) used for 130 extraction were used as negative controls. A representative extract was used as a quality 131 control (QC) sample, and this QC sample was analyzed every twelve samples to monitor 132 retention time shift and intensity shift. 133 134 3D mass spectral molecular cartography 135 136 Dried extracts were dissolved in 50/50 vol/vol methanol (Fisher Scientific, HPLC 137 Grade)/acetonitrile (Fisher Scientific, Optima LC/MS) to a concentration of 1 mg/ml, 100 µL 138 of each extract were transferred to a 96-well plate (Falcon, 96-well plates, 0.34 ml, 139 polypropylene), sealed with Zone-Free Sealing Film (Excel Scientific) and centrifuged for 30 140 min. at 2000 r.p.m. at 4◦C. 20 µL of each extract were injected into the LC-MS/MS equipment. 141 MS analysis was performed on a micrOTOF-Q II (Bruker Daltonics) mass spectrometer with 142 an electrospray ionization (ESI) source, controlled by OTOF control and Hystar.
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