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In our simulations for the autotrophs, we varied two of the three trade-off properties (level of defence, plasticity costs and defence costs; see Fig. 1b) at a time and kept the third one constant. This results in three constellations reflecting three different trade-offs between these properties (Table 1):

parallel: trade-off between defence and plasticity costs;

crossing: trade-off between defence costs and plasticity costs;

angle: trade-off between defence and defence costs.

Table 1 Description of the three constellations parallel, crossing, and angle defining the position of the four phenotypes in the trait space of defence and growth rate.Full size tableIn all three constellations, the autotrophic species B spanned the entire defence range, i.e. it had a completely undefended phenotype Bu and a maximally defended phenotype Bd. A either had a more limited defence range (in constellations parallel and angle) or spanned the entire range as well (in constellation crossing), representing three distinct ways that the trade-off between defence, growth rate, and plasticity range may play out. For each constellation, we varied the maximum switching rate χmax over 5 orders of magnitude to investigate the effect of plasticity (Table 1, middle row). This parameter determines how rapidly a species can switch between phenotypes (see “Methods”, “Exchange rates”); higher values indicate faster adaptation. These results were also compared with a non-plastic baseline scenario where both phenotypes of each species are presented but χmax = 0 (Table 1, upper row), as well as a rigid scenario where the species have only a single phenotype (Table 1, bottom row). All parameters and their values can be found in Supplementary Table S1.In the following, we give a detailed description of the results for constellation parallel, where the autotroph species A and B have the same defence costs resulting in parallel trade-off lines between defence and growth rate, while varying the level of defence for A and varying the plasticity costs for B (Table 1, left column). We start with examining patterns for the phenotype biomasses, coexistence and community stability in the non-plastic baseline scenario “parallel 0”, and then compare the corresponding scenarios with a low exchange rate (“parallel 0.01”) and a high exchange rate (“parallel 1”). We next discuss the other two constellations (crossing and angle, Table 1) more briefly. Finally, we generalize across all scenarios and focus on the coexistence, the degree of maladaptive switching, and the consumer and total autotroph biomasses.Non-plastic baseline dynamics: scenario parallel 0
In this scenario, four single phenotypes unconnected by exchange compete with each other. Thus, species coexistence here depends entirely on phenotype coexistence: the trade-offs have to be such that for each species, at least one phenotype is a good enough competitor to survive. Which phenotypes survive depend on the two trade-off parameters, defence of the defended phenotype of species A (dAu) and plasticity costs for species B (pcB), which thus determine whether coexistence is possible.The defence costs were kept constant at an intermediate value of 0.3 for both species, resulting in parallel trade-off lines (Table 1, scenario “parallel 0”). The undefended phenotype of A, Au, is a growth-specialist with the highest growth rate of all phenotypes. The defended phenotype of the same species, Ad, has a defence between 0 and 0.9 and a relatively high growth rate, and can be viewed as a generalist. Species B has variable plasticity costs that lower the growth rate of both phenotypes. The defended phenotype of species B, Bd, has the lowest growth rate of all phenotypes but is very well-defended, and thus a defence-specialist. Its undefended phenotype, Bu, is as undefended as Au but has a lower growth rate; it is thus always an inferior competitor and inevitably goes extinct (Fig. 2c).Figure 2Biomasses, coexistence and trait space for scenario parallel 0. Biomasses of the four autotrophic phenotypes (a–d), their coexistence patterns (e), the consumer biomass (f) and the autotrophs’ trait values (g–j) (higher biomasses are shown by darker colours). Lines in (a–f) separate the regions I–III of different coexistence patterns. Note that in (a–f), the y-axis is reversed to show increasing fitness along all axes. An exemplary trait combination for every region is shown in (g–j); larger symbols indicate the surviving phenotypes. Shaded areas in (e) depict oscillating systems (quarter-lag predator–prey cycles in dense shading, antiphase cycles in loose shading).Full size imageAs Bu never survives, coexistence of the autotroph species requires the survival of defence-specialist Bd. Bd can only survive if Ad is not too defended, because Ad has a higher growth rate than Bd and will outcompete Bd in the “defended” niche otherwise (region Ib; Fig. 2d,h). A second criterion is that the plasticity costs for B must not be too high, because then the benefits of the defence of Bd no longer outweigh the costs, and it will go extinct even if there are no other highly defended phenotypes around (region Ia; Fig. 2d,g). In the regions where Bd goes extinct, species coexistence is not possible (Fig. 2e). The generalist Ad either survives by itself (region Ia in Fig. 2b,g) if its defence is low to intermediate, or together with the growth-specialist Au if its defence is high (region Ib in Fig. 2a,b,h). In the regions II and III where Bd survives, it never survives on its own, but always together with one of the phenotypes of A. It coexists with the growth-specialist Au if the plasticity costs are very low (region II in Fig. 2,i), and together with Ad if they are low to intermediate (region III in Fig. 2,j). These two regions do support species coexistence (Fig. 2e).In three of the four regions (Ib, II and III in Fig. 2f), consumer biomass is low, because the final community always contains a well-defended phenotype (Ad in region Ib, and Bd in regions II and III); the overall level of defence of the community is relatively high in these regions (Supplementary Figure S1). Conversely, consumer biomass is relatively high in region Ia, because the only surviving autotroph phenotype is relatively fast-growing and fairly undefended (Fig. 2f,g). The regions where a well-defended phenotype survives often show antiphase cycles (Ib, II and III in Fig. 2e). These cycles do not occur in the region where only Ad survives (Ia in Fig. 2e); but regular quarter-lag predator–prey cycles can be found here if Ad is almost entirely undefended.While the community defence (i.e. mean defence of the autotroph community) depends strongly on the coexisting phenotypes, the community growth rate is roughly constant because over the entire trait space, at least one phenotype with a high growth rate always survives (Supplementary Figure S1). The standing variance of the community defence was high when two phenotypes coexist as they occupy different niches along the defence axis (Fig. 2h–j). In contrast, the variance of the community growth rate was very low and almost constant across all regions.Effect of phenotypic plasticityEven a little bit of plasticity in the scenario parallel 0.01 (χmax = 0.01) can change the above patterns for coexistence, stability, and average consumer biomass (Fig. 3a–d). While the autotrophs are intuitively expected to benefit from being plastic, the effect of plasticity on consumer biomass always turned out to be positive (Fig. 3a). This may be explained by the fact that switching was always, on average, maladaptive (Fig. 3c,d), measured by the adaptation index Φ (see Eqs. (11–13) in “Methods”). This index combines information on the net “flow” of individuals due to switching (i.e. whether more undefended individuals switch to defended or vice versa) with the fitness difference between the two phenotypes, and thus measures whether overall, more individuals switch from a low-fitness to a high-fitness phenotype (adaptive) or the reverse (maladaptive). This index can approach zero, but is always negative at equilibrium (see Appendix B), indicating maladaptive switching.Figure 3Consumer biomass, autotroph coexistence and maladaptive switching for the scenarios parallel 0.01 (a–d) and parallel 1 (e–h). Consumer biomass (a,e), the autotroph coexistence patterns (b,f), and the autotrophs’ maladaptive switching Φ (c,d,g,h) (higher biomasses or more intensive maladaptive switching are shown by darker colours). Lines separate the regions I–III of different autotroph coexistence. The y-axis is reversed to follow the pattern of increasing fitness. Grey areas in (c,d,g,h) depict areas where the species was extinct. Shaded areas in b and f depict oscillating systems (quarter-lag predator–prey cycles in dense shading, antiphase cycles in loose shading).Full size imageThe most striking effect of plasticity was on coexistence, which was affected both positively and negatively by plasticity in different regions of the parameter space (Fig. 3b, Supplementary Figure S4a–d). A negative effect on coexistence is seen in region II, where the autotroph species previously coexisted (Fig. 2e), while with plasticity, B outcompeted A (Fig. 3b). Without plasticity, coexistence was possible in this region because Au and Bd survived; importantly, Au outcompeted Bu due to its higher growth rate, even though the difference between their growth rates is very small in this region (Fig. 2i). Plasticity reverses the competitive exclusion pattern between the two undefended phenotypes: Bu receives a constant flow of biomass from the well-defended Bd, which compensates for its slightly lower growth rate and allows it to outcompete Au. Thus, coexistence is reduced as a direct consequence of maladaptive switching.Plasticity can also promote coexistence, as the coexistence region now extends into former region Ib where the generalist Ad is highly defended (Fig. 2b, Supplementary Figure S1a). This is also an effect of maladaptive switching, though in this case the effect is indirect, mediated through the effect of plasticity on consumer biomass. Without plasticity, coexistence was impossible in region Ib because Bd was always outcompeted by Ad: even though the latter had a slightly lower level of defence, this was outweighed by its higher growth rate, making Ad the superior competitor over Bd. However, plasticity changes this because maladaptive switching increases the consumer biomass, which in turn alters the cost/ benefit balance of defence: Bd derives a stronger benefit from its high level of defence, which now outweighs the cost and allows it to survive. Coexistence through this mechanism is not possible when the plasticity costs for B are too high or when Ad is too well-defended, explaining the narrowing of the coexistence “tail” for high defence of Ad (Fig. 3b).While the patterns of coexistence changed when allowing for plasticity, the patterns in the trait values were nearly indistinguishable from the previous scenario (Supplementary Figure S1, S2). Finally, plasticity had a strong impact on the community dynamics, as most of the antiphase cycles were stabilized (Ib, II, III in Fig. 3b). Their area decreased sharply as these cycles were characterized by asynchronous dynamics between the two prey phenotypes, which were reduced by plasticity. In contrast, the area of the quarter-lag predator–prey cycles remained unaffected by plasticity.All the above patterns were found to a far stronger degree with a higher amount of plasticity (χmax = 1; Fig. 3e–h, Supplementary Figure S4e–h). Consumer biomass increased strongly everywhere (cf. Fig. 3a,e), reflecting the strong increase in the degree of maladaptive switching (cf. Fig. 3c,d,g,h). The higher exchange rates led to more synchronization between the phenotypes, extinguishing the antiphase cycles completely (Fig. 3f). It also decreased the biomass of both defended phenotypes (cf. Supplementary Figure S4b,d,f,h). This in turn led to a lower community defence and a higher community growth rate (Supplementary Figure S3) both contributing to a higher consumer biomass. Finally, there was a sharp decrease in the coexistence region for high plasticity (Fig. 3e). Region II, where B outcompetes A through maladaptive switching, doubled in size due to the much higher degree of maladaptive switching (Fig. 3g,h). Region I, where A outcompetes B, now also increased, when the level of defence of Ad is relatively low (Fig. 3e). This is again an indirect effect of maladaptive switching causing a strong increase in consumer biomass, affecting the cost/ benefit balance of defence: while Bd derives a strong benefit from its high level of defence, Bu is completely undefended, and is at an extra disadvantage because of its low growth rate. Thus, while Bd would have been able to survive by itself, the high exchange rate causes a strong source-sink dynamic that drives B extinct.Effect of plasticity in constellations crossing and angle
In constellation crossing the trade-off lines of both species cross in the trait space, as the level of defence is the same for both defended phenotypes; species B has a lower growth rate for its undefended phenotype than species A due to plasticity costs, while its defence costs are low and thus the growth rate of its defended phenotype is higher than for species A (Table 1, Supplementary Figure S5). Without plasticity the crossing trade-off lines lead to coexistence of both species in all simulations as Au and Bd were always the only survivors, mostly showing antiphase oscillations (Supplementary Figure S5).Allowing for phenotypic plasticity has the same results as were observed for constellation parallel: consumer biomass sharply increases (Fig. 4a,e); antiphase cycles are dampened or absent; and the area of coexistence decreases (Fig. 4b,f). All these changes are more pronounced for higher exchange rates (cf. Fig. 4a,b,e,f). Again, the biomass of the defended phenotypes decreased for high exchange rates (Supplementary Figure S6). Switching was always maladaptive for high exchange rates (Fig. 4g,h), and mostly maladaptive for low exchange rates (Fig. 4c,d). As was seen for constellation parallel, maladaptive switching was the reason for the decrease in coexistence. B can outcompete A when B has low plasticity costs. Bd has a much higher growth rate than Ad, while the undefended phenotypes have similar growth rates. The direction of competitive exclusion between Au and Bu is thus easily reversed by Bd donating biomass to the sink Bu, allowing B to occupy both niches and outcompete A (region II in Fig. 4b,f). The same mechanism happens in reverse for high plasticity and defence costs of B: the differences in growth rate for the undefended phenotypes are high, while the defended phenotypes have very similar growth rates. Au can support Ad, and A outcompetes B (region III in Fig. 4b,f).Figure 4Coexistence and maladaptive switching for scenario crossing 0.01 (a-d) and crossing 1 (e–h). Consumer biomass (a,e), the autotroph coexistence patterns (b,f), and the autotrophs’ maladaptive switching Φ (c,d,g,h) (higher biomasses or more intensive maladaptive switching are shown by darker colours). Lines separate the regions I–III of different autotroph coexistence. The x- and y-axis are reversed to follow the pattern of increasing fitness. Shaded areas in (b) depict antiphase cycles. Grey areas in (c,d,g,h) depict areas where the species was extinct. Shaded grey areas depict areas without simulations (cf. “Methods”). Note that (c,d,g,h) have each a different colour scale.Full size imageIn constellation angle there are no plasticity costs, and thus the undefended phenotypes Au and Bu have identical growth rates. The defended phenotypes take the same places in trait space as in the parallel constellation: Ad is a generalist, with a lower level of defence and a relatively high growth rate due to low defence costs, whereas Bd is a defence-specialist with a high level of defence but a low growth rate. This leads to the trade-off lines forming an angle (see Table 1). Without phenotypic plasticity, the coexistence patterns are the same as in constellation parallel, except that no competitive exclusion occurs between the undefended phenotypes; instead, they (neutrally) coexist in regions Ib, II and III (Supplementary Figure S7; cf. Fig. 2).With plasticity, neutral coexistence vanished: the defended phenotype that survived (Ad in region Ib, Bd in region III) could support the undefended phenotype of its own species, driving the other species extinct (Fig. 5b,f). As in the other constellations, the area of coexistence and the biomasses of the defended phenotypes decreased and antiphase cycles vanished with increasing χmax (Fig. 5b,f, Supplementary Figure S8), while maladaptive switching and the consumer biomass increased (Fig. 5).Figure 5Coexistence and maladaptive switching for scenario angle 0.01 (a–d) and angle 1 (e–h). Consumer biomass (a,e), the autotroph coexistence patterns (b,f), and the autotrophs’ maladaptive switching Φ (c,d,g,h) (higher biomasses or more intensive maladaptive switching are shown by darker colours). Lines separate the regions I–III of different autotroph coexistence. The y-axis is reversed to follow the pattern of increasing fitness. Shaded areas in (b) depict antiphase cycles. Grey areas in (c,d,g,h) depict areas where the species was extinct. Note that (c,d,g,h) have each a different colour scale.Full size imageGeneral resultsAs plasticity had very similar effects across all three constellations, we here generalize our results: we compare the three constellations for exchange rates over 5 orders of magnitude, as well as the non-plastic scenario and the rigid scenario (Table 1). That is, all simulations from one scenario (e.g. parallel 0) were summarized into one bar respective point in Fig. 6.Figure 6General patterns for coexistence, maladapative switching and biomasses. Share of surviving species in percent (A, B, coexistence or neutral coexistence) (a–c), median absolute value of maladaptive switching Φ (d–f) and median of total autotroph biomass (A + B), median consumer biomass C and share of defended phenotypes ((Ad + Bd)/(A + B)) (g–i) for the three constellations and increasing maximum exchange rates χmax. χmax = 0 denotes the non-plastic scenarios; *denotes the rigid scenarios. Maladaptive switching and the share of defended phenotypes do not apply for the rigid scenarios.Full size imageFor all constellations, the fraction of simulation runs leading to coexistence was highest in the non-plastic scenario and decreased with increasing χmax (Fig. 6a–c). In constellation parallel the share of coexistence for increasing χmax continuously decreased from 51 to 3% (Fig. 6a). In crossing, the share decreased from full to no coexistence (Fig. 6b). In angle, the share of coexistence was 88% in the non-plastic scenario when taking also neutral coexistence into account (Fig. 6c). Its share decreased to 9% for a χmax of 10 and increased again to 25% for the rigid scenario. Maladaptive switching increased for both species and all constellations for increasing χmax (Fig. 6d–f). The increased plasticity led to a lower total autotroph biomass and a lower share of defended phenotypes (Fig. 6g–i), which resulted in higher consumer biomass (Fig. 6g–i).Interestingly, and counterintuitively, the above patterns show that increasing the speed of plasticity (by increasing χmax) makes the system behave more like the rigid system. The coexistence patterns in scenarios with high χmax approach those of the rigid scenarios in two of the constellations (Fig. 6a,b). Similarly, the total autotroph and consumer biomasses approach the ones in the rigid scenarios (Fig. 6g–i). Thus, we found the higher χmax make the autotrophs not more adaptive, but behave more like non-adaptive species. More

Insects and plantsLarvae of fall armyworm (FAW, Spodoptera frugiperda) were cultured at the Department of Entomology at the Max Planck Institute for Chemical Ecology, and reared on a semi-artificial diet based on pinto bean59, and maintained under controlled light and temperature conditions (12:12 h light/dark, 21 °C).Feeding experiments3rd–4th instar FAW larvae were utilized for all experiments. Insects were starved overnight prior to feeding experiments. The following day insects were fed with a semi-artificial, pinto bean-based diet or put on maize leaves in small plastic cups and allowed to feed on the respective diets for a day. Insects were dissected in cold phosphate buffered saline (PBS, pH = 7.4) to harvest larval tissues (guts, Malphigian tubules, fat bodies, cuticle), which were stored at − 80 °C until further use. For droplet feeding, 12.5 mM DIMBOA was prepared by dissolving the compound in DMSO. This DIMBOA solution was further diluted in 10% aqueous sucrose solution. The larvae were stimulated with forceps to encourage regurgitation, and 2 μL DIMBOA-sucrose solution was administered directly to the larval mouthparts. Insects were then fed on semi-artificial diet for up to 6 h; following which gut tissue was dissected using cold phosphate buffer and the tissue samples were stored at − 80 °C until further use.Insect cell culturesSpodoptera frugiperda Sf9 cells and Trichoplusia ni Hi5 cells were cultured in Sf-900 II serum-free medium (Gibco) and ExpressFive serum-free medium (Gibco), respectively. Adherent cultures were maintained at 27 °C, and sub-cultured every 3–4 days.Cell treatmentsInsect cells were seeded in 6 well culture plates (Corning) and left at 27 °C overnight. For transcript stability tests, a fresh cycloheximide (CHX) stock (50 mg/mL) was prepared in ethanol and added to the cultured cells at a concentration of 50 µg/mL. Incubations with CHX were performed up to 6 h. For testing substrate specificity, cells were then treated with the following compounds for 1 h—DIMBOA (25–100 μM), indole (50–100 μM), quercetin (50–100 μM), and esculetin (50–100 μM). All the stocks were prepared in DMSO and cells treated with the corresponding volume of pure DMSO served as a control. The range of concentrations used for the substrates was based on previous work38.RNA extraction, reverse transcription and real time-PCR analysisTissue samples from the larvae were homogenized and total RNA extracted using the innuPREP RNA Mini Kit (Analytik Jena). Cell cultures used for RNA extraction were obtained during sub-culturing at full confluency, and centrifuged at 500×g for 5 min. The culture medium was discarded, and the fresh pellets were directly used for RNA extraction. RNA concentrations were measured with the NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific). First strand cDNA was synthesized from 1 μg total RNA using SuperScript III Reverse Transcriptase and OligodT primers from Invitrogen. Sequences were successfully amplified using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 35 cycles of 10 s at 98 °C, 20 s at 55 °C, 45 s at 72 °C; and 5 min at 72 °C). The PCR products were purified with a PCR cleanup kit (Qiagen) and cloned into pCR-Blunt II-TOPO vector (Life Technologies) and transformed into NEB cells (Life Technologies), which were plated on selective LB agar medium containing 100 μg/mL ampicillin and incubated overnight at 37 °C. Positive colonies were identified by PCR using vector-specific M13 primers. Positive clones were confirmed by sequencing. Real time PCR analyses were carried out using Brilliant III SYBR Master Mix, employing SYBR Green chemistry. Relative quantification of the transcript levels was done using the 2−∆∆Ct method60. SfRPL10 was used as reference gene for all analyses. The primer pairs used for distinguishing between the variants are listed in Supplementary Table 1. As the expression of full-length and variants of SfUGT33F28 differed according to the strains, tissues, and treatments being analyzed, variant expression is reported as ratios relative to the canonical transcript to facilitate comparisons.Preparation of minigenes for alternative splicing studiesGenomic DNA was isolated from S. frugiperda larvae using the cetyl trimethyl ammonium bromide (CTAB) protocol61. DNA concentration was measured with the NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific). The minigene was amplified using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 35 cycles of 10 s at 98 °C, 30 s at 55–60 °C, 1 min 30 s at 72 °C; and 10 min at 72 °C), cloned into a pCR-Blunt II-TOPO vector (Life Technologies) and sequenced using M13 primers. The confirmed sequence was eventually cloned into a pIB/V5-His-TOPOvector (Life Technologies) and transformed into NEB cells (Life Technologies). Positive colonies were identified by colony PCR using vector-specific OpIE2 primers, sub-cultured overnight at 37 °C in liquid LB medium containing 100 μg/mL ampicillin and used for plasmid DNA purification with the NucleoSpin Plasmid kit (Macherey-Nagel). Concentration and purity of the obtained construct was assessed by the NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific) and the correct orientation of the PCR products was confirmed by DNA sequencing.Nuclear protein isolationNuclear proteins were isolated from insect cells62 using the protocol originally described with few modifications. Cells grown to concentrations of up to 1 × 106 cells/well were harvested and washed with PBS (pH 7.4). The extracts were centrifuged at 12,000×g for 10 min and pellets were re-suspended in 400 μL cell lysis buffer (10 mM HEPES, pH 7.5, 10 mM KCl, 0.1 mM EDTA pH 8.0, 1 mM DTT, 0.5% Nonidet-40 and 10 μL protease inhibitor cocktail). Cells were allowed to swell on ice for 20 min with intermittent mixing. Suspensions were vortexed to disrupt the cell membranes and then centrifuged at 12,000×g for 10 min at 4 °C. Pelleted nuclei were washed thrice with cell lysis buffer, re-suspended in 50 μL nuclear extraction buffer (20 mM HEPES pH 7.5, 400 mM KCl, 1 mM EDTA pH 8.0, 1 mM DTT, 10% glycerol and protease inhibitor) and incubated on ice for 30 min. Nuclear fractions were collected by centrifugation at 12,000g for 15 min at 4 °C. Protein concentrations were measured by Bradford and extracts were stored at − 80 °C until further use.Electrophoretic mobility shift assay (EMSA)EMSA was performed using the LightShift Chemiluminescent EMSA kit (Thermo Scientific) following the manufacturer’s instructions. Genomic DNA fragments of 20–25 bp corresponding to the 5′ flanking region of UGT33F28 exon 1 (with and without AhR-ARNT motif deletion) were synthesized with covalently linked biotin (Sigma). The DNA probes used in the experiment are listed in Supplementary Table 6. EMSA was performed in 20 µL reactions containing 20 fmol biotinylated DNA probe with 3.5–4 µg nuclear protein extracted from insect cells, according to manufacturer’s instructions. A reaction comprising the above along with the excess of unlabeled canonical DNA probe (200 molar excess) was further employed as a control. The reaction was assembled at room temperature and incubated for 30 min. The reactions were separated on a 5% TBE gel in 0.5X TBE at 100 V for 60 min. The samples were then transferred to a positively charged nylon membrane (Hybond N+, Amersham Bioscience) using semi-dry transfer at 15 V for 30 min. The membrane was cross-linked for 1 min using the auto cross-link function on the UV cross-linker (Stratagene). The biotinylated DNA–protein complex was detected by the streptavidin–horseradish peroxidase conjugated antibody provided in the kit. The membrane was washed and incubated with the chemiluminescence substrate for 5 min and the signals were developed by exposing the membrane to an X-ray film for 1 min.Streptavidin affinity purificationStreptavidin agarose (Sigma-Aldrich) was employed for protein purification. Briefly, 50–100 μL of agarose was packed into a 1.5 mL Eppendorf tube for each sample. The agarose was allowed to settle with a short centrifugation (500×g, 5 min) and the supernatant was discarded. The agarose was washed 4–5 times with binding buffer (PBS containing 1 mM EDTA, 1 mM DTT, 4 µg poly dI. dC as non-specific competitor DNA and protease inhibitor). Simultaneously, the binding reaction with the nuclear protein fraction and the DNA probe was assembled as described above. A 100 μg amount of total nuclear protein was incubated with 4 μg of biotinylated DNA probe at room temperature for 20 min. The reaction was loaded onto the streptavidin column equilibrated with the binding buffer and incubated for another 1 h at room temperature with gentle shaking. Subsequently, the agarose was washed 4–5 times with the binding buffer. After the final wash, the supernatant was aspirated and 10 μL was left above the beads. For protein separation, 20–30 μL pf the SDS loading buffer was added onto the agarose, boiled at 95 °C for 5 min and the sample thus obtained was utilized for electrophoresis.Deletion mutagenesisFor deletion mutagenesis, a pair of primers flanking the sequence to be deleted (non-overlapping) was designed. The pCR-Blunt II-TOPO vector (Life Technologies) clone for the SfUGT33F28 exon 1–2 minigene was utilized as a template. Sequence was successfully amplified using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 20 cycles of 10 s at 98 °C, 30 s at 55–60 °C, 4 min at 72 °C; and 10 min at 72 °C). A DpnI digest was performed to remove the background DNA, followed by ligation and transformation into fresh cells. The sequence of the mutant TOPO clone was then confirmed and utilized as a template for cloning into pIB/V5-His-TOPO vector (Life Technologies) for transfection into insect cells.Cloning and heterologous expression of SfUGTsSequences were amplified from S. frugiperda gut cDNA samples using Phusion High Fidelity DNA Polymerase (New England Biolabs) (PCR protocol: 30 s at 98 °C; 35 cycles of 10 s at 98 °C, 20 s at 55–60 °C, 45 s at 72 °C; and 5 min at 72 °C). The resulting amplified products were purified with a PCR cleanup kit (Qiagen) and incubated with GoTaq DNA polymerase (Promega) for 15 min at 72 °C in order to add A overhangs. The products were cloned into the pIB/V5-His-TOPO vector (Life Technologies) and transformed into NEB cells (Life Technologies), which were plated on selective LB agar medium containing 100 μg/mL ampicillin and incubated overnight at 37 °C. Positive colonies were identified by PCR using vector-specific OpIE2 primers, sub-cultured overnight at 37 °C in liquid LB medium containing 100 μg/mL ampicillin and used for plasmid DNA purification with the NucleoSpin Plasmid kit (Macherey-Nagel). Concentration and purity of the obtained constructs were assessed by NanoDrop 2000 UV–Vis Spectrophotometer (Thermo Scientific) and the correct orientation of the PCR products was confirmed by DNA sequencing.Insect cell transfectionFor transfection, Sf9 cells and Hi5 cells were sub-cultured at full confluency in a 6-well plate in a 1:3 dilution and left overnight to adhere to the flask surface. The medium was replaced, and transfections were carried out using FuGENE HD Transfection Reagent (Promega) in a 1:3 plasmid/lipid ratio (1.7 μg plasmid and 5.0 μL lipid for 3 mL medium). Cells were incubated for 48–72 h at 27 °C and re-suspended in fresh medium containing 50 μg/mL blasticidin for 2 weeks. Stable cell cultures were subsequently maintained at 10 μg/mL blasticidin.Cell lysate preparationCells were obtained from cultures 2 weeks post transfection growing stably on 50 μg/mL blasticidin. A 1 mL quantity of cells was harvested for each construct and re-suspended into 100 µL buffer. Protein concentrations were measured using the Bradford reagent, and 1–2 μg of the cell lysate was used for enzyme assays.Microsome preparationFor microsome extraction, confluent, stably transfected cells from five T-75 flasks (10 mL culture) per recombinant plasmid were harvested by scraping the cells off the bottom using a sterile cell scraper (Sarstedt AG, Nuembrecht, Germany). The obtained cell suspensions were combined into a 50 mL falcon tube and centrifuged at 1000×g for 15 min at 4 °C (AvantiTM J-20 XP Centrifuge, Beckman Coulter, Krefeld, Germany). The supernatant was discarded, the cells were washed twice with ice-cold PBS buffer (pH 7.4) and centrifuged at 1000×g for 15 min. The resulting cell pellet was re-suspended in 10 mL hypotonic buffer (20 mM Tris, 5 mM EDTA, 1 mM DTT, 20% glycerol, pH 7.5), containing 0.1% BenzonaseR nuclease and 100 μL Protease Inhibitor Cocktail (Serva) followed by incubation on ice for 30 min. After cell lysis, the cells were homogenized by 20–30 strokes in a Potter–Elvehjem tissue grinder (Kontes Glass Co., Vineland, USA) and were subsequently mixed with an equal volume of sucrose buffer (20 mM Tris, 5 mM EDTA, 1 mM DTT, 500 mM sucrose, 20% glycerol, pH 7.5). The homogenate was centrifuged at 1200×g and 4 °C for 10 min (AvantiTM J-20 XP Centrifuge, Beckman Coulter), and the supernatant was transferred into Beckman polycarbonate ultracentrifugation bottles (25 × 89 mm) (Beckman Coulter) and centrifuged at 100,000×g and 4 °C for 1.5 h in a fixed angle Type 70 Ti rotor (OptimaTM L-90K Ultracentrifuge, Beckman Coulter). After ultracentrifugation, the clear supernatant, containing the cytosolic fraction, was aliquoted into 1.5 mL Eppendorf tubes. The pellet, containing the microsomal fractions, was re-suspended in 1 mL of phosphate buffer (100 mM K2HPO4, pH 7.0), containing 10 μL Protease Inhibitor Cocktail (Serva) and stored at − 80 °C until further use. Typically, 5–10 μg of the microsome fraction so obtained was utilized for the enzyme assays.Cross-linking assaysCross-linking assays were performed using dimethyl suberimidate (DMS) as the cross-linking agent. A fresh stock of DMS (5 mg/mL) was prepared in 0.2 M triethanolamine (pH 8.0) at the start of each assay. DMS was added to a final concentration of 2.5 mg/mL to insect cell microsomes with gentle shaking up to 3 h, and samples were subsequently stored at − 20 °C until further use. All protein samples were electrophoresed using a 12% Mini-PROTEAN tris glycine gel, blotted onto PVDF membrane using wet transfer at 70 V for 30–45 min, followed by detection using the V5-HRP conjugate.V5-based affinity purificationAnti-V5 agarose affinity gel (Sigma-Aldrich) was employed for protein purification. Briefly, 50–75 μL of the agarose was packed into a 1.5 mL Eppendorf tube for each sample. The agarose was allowed to settle with a short centrifugation and the supernatant was discarded. The agarose was washed 4–5 times with PBS (pH 7.4). Samples to be purified were incubated with 5% digitonin on ice for 20 min and subject to centrifugation at 16,000×g for 30 min. Clarified cell lysate or microsomal extract was added onto the resin (up to 200 μL, volume adjusted by addition of PBS) and incubated for 1.5 h on a shaker. Subsequently, the agarose was washed 4–5 times with PBS. After the final wash, the supernatant was aspirated and 10 μL was left above the beads. This fraction was used for both protein electrophoresis and enzyme assays (separate purifications). For SDS-PAGE, 20–30 μL pf the SDS loading buffer was added onto the agarose, boiled at 95 °C for 5 min and sample thus obtained was utilized for electrophoresis.LC–MS/MS peptide analysisProtein bands of Coomassie Brilliant blue R250 stained gels were cut from the gel matrix and tryptic digestion was carried out63. For LC–MS/MS analysis of the resulting peptides, samples were reconstituted in 20 μL aqueous 1% formic acid, and 1 μL was injected onto an UPLC M-class system (Waters, Manchester, UK) coupled to a Synapt G2-si mass spectrometer (Waters, Manchester, UK). Samples were first pre-concentrated and desalted using a Symmetry C18 trap column (100 Å, 180 µm × 20 mm, 5 µm particle size) at a flow rate of 15 µL/min (0.1% aqueous formic acid). Peptides were eluted onto a ACQUITY UPLC HSS T3 analytical column (100 Å, 75 µm × 200 mm, 1.8 µm particle size) at a flow rate of 350 nL/min with the following gradient: 3–15% over 3 min, 15–20% B over 7 min, 20–40% B over 30 min, 40–50% B over 5 min, 50–70% B over 5 min, 70–95% B over 3 min, isocratic at 95% B for 1 min, and a return to 1% B over 1 min. Phases A and B were composed of 0.1% formic acid and 100% acetonitrile in 0.1% formic acid, respectively). The analytical column was re-equilibrated for 10 min prior to the next injection. The eluted peptides were transferred into the mass spectrometer operated in V-mode with a resolving power of at least 20,000 full width at half height FWHM. All analyses were performed in a positive ESI mode. A 100 fmol/μL sample of human Glu-Fibrinopeptide B in 0.1% formic acid/acetonitrile (1:1 v/v) was infused at a flow rate of 1 μL/min through the reference sprayer every 45 s to compensate for mass shifts in MS and MS/MS fragmentation mode. Data were acquired using data-dependent acquisition (DDA). The acquisition cycle for DDA analysis consisted of a survey scan covering the range of m/z 400–1800 Da followed by MS/MS fragmentation of the ten most intense precursor ions collected at 0.5 s intervals in the range of 50–2000 m/z. Dynamic exclusion was applied to minimize multiple fragmentations for the same precursor ions. MS data were collected using MassLynx v4.1 software (Waters, Manchester, UK).Data processing and protein identificationDDA raw data were processed and searched against a sub-database containing common contaminants (human keratins and trypsin) using ProteinLynx Global Server (PLGS) version 2.5.2 (Waters, Manchester, UK). Spectra remaining unmatched by database searching were interpreted de novo to yield peptide sequences and subjected to homology-based searching using the MS BLAST program64 installed on a local server. MS BLAST searches were performed against a Spodoptera frugiperda database obtained by in silico translation of the S. frugiperda transcriptome37 and against arthropoda database (NCBI). PKL-files of MS/MS spectra were generated and searched against Spodoptera frugiperda database combined with NCBI nr (downloaded on May 24, 2020) using MASCOT software version 2.6.2. The following searching parameters were applied: fixed precursor ion mass tolerance of 15 ppm for the survey peptide, fragment ion mass tolerance of 0.1 Da, 1 missed cleavage, fixed carbamidomethylation of cysteines and possible oxidation of methionine.Enzymatic assaysFor UGT assays, samples from insect cell cultures (transient or stable) were prepared in phosphate buffer (pH 7.0, 100 mM). Typical enzyme reactions included 5–10 µg cell microsomal extracts, 2 μL of 12.5 mM DIMBOA in DMSO (25 nmol), 4 μL of 12.5 mM UDP-glucose in water (50 nmol), and phosphate buffer (pH 7.0, 100 mM) to give an assay volume of 50 μL. Controls containing either boiled enzymatic preparation, or only the protein suspension and buffer were included. After incubation at 30 °C for 60 min, the enzyme reactions were interrupted by adding 50 μL of 1:1 (v:v) methanol/formic acid solution. For enzyme assays involving resin purified microsomal extracts, equal amounts of extracts were employed for resin purification and the enzyme assay (buffer + substrate) was pipetted directly onto the resin. Post incubation, samples were centrifuged, supernatant was collected, and reaction was stopped by addition of methanol/formic acid solution. Assays were centrifuged at 5000g for 5 min and the obtained supernatant was collected and analyzed by LC–MS/MS.Chromatographic methodsFor all analytical chromatography procedures, formic acid (0.05%) in water and acetonitrile were used as mobile phases A and B, respectively, and the column temperature was maintained at 25 °C. Analyses of enzymatic assays and plant samples used a Zorbax Eclipse XDB-C18 column (50 × 4.6 mm, 1.8 μm, Agilent Technologies) with a flow rate of 1.1 mL/min and with the following elution profile: 0–0.5 min, 95% A; 0.5–6 min, 95–67.5% A; 6.02–7 min, 100% B; 7.1–9.5 min, 95% A. LC–MS/MS analyses were performed on an Agilent 1200 HPLC system (Agilent Technologies) coupled to an API 6500 tandem spectrometer (AB Sciex) equipped with a turbospray ion source operating in negative ionization mode. Multiple reaction monitoring (MRM) was used to monitor analyte parent ion to product ion conversion with parameters from the literature for DIMBOA65 and DIMBOA-Glc16. Analyst (version 1.6.3, Applied Biosystems) software was used for data acquisition and processing.Statistical analysisAll statistical analyses were carried out using SigmaPlot 12.0 and R studio (version 3.6.3). Data were tested for homogeneity of variance and normality and were appropriately transformed to meet these criteria where required. The specific statistical method used for each data set is described in the figure legends. More

Experimental design and crop managementField experiments were conducted at Chengyang Agricultural Experimental Station, Qingdao, China (36°18′ 11″/N, 120°21′ 13″/E) in 2019 and 2020. The soil type in the field was brown loam that contained 22.76 g kg−1 organic matter, 82.39 mg kg−1 alkali-hydrolysable N, 25.10 mg kg−1 Olsen-P and 94.89 mg kg−1 exchangeable K. The test cultivars of maize were Jinhai5 with strong lodging resistance and Xundan20 with weak lodging resistance, which were repeated four times in plots laying out in randomized block designs. Plant density was 7.5 plants / m2 with the row spacing of 60 cm. the plot consisted of 8 rows length of 15 m. Two–three seeds per hole were manually sowed at 5 cm on 20 April 2019 and 24 April 2020, and the seedlings were thinned to the target planting density at V2, and harvested on 10 September and 14 September, respectively. Fertilization and irrigation management followed local production practices in maize.Sampling and measurementPlant samples were taken at V8, V12, R1, R2 and R6. Ten typical plants of each tested cultivars were selected to be subjected to mechanical and above-ground morphological measurements at each sampling. The other three maize plants were used to measure morphological traits of roots. Xundan20 was seriously damaged due to the storm in the late stage of maize growth in 2020, resulting in the missing data for physiological maturity.Determination of leaf area vertical distributionLeaf area of expanded leaves each was computed by the coefficient method: Single leaf area = length * width * 0.75. Leaf area for unexpanded leaves was estimated by the leaf weight method. Leaf area per plant was the sum of all individual green leaf areas. Leaf height is the height from the ground to the leaf collar position of maize.Determination of max root side-pulling resistanceSample plants were surrounded with water-proof steel devices inserted into underground, and watered to soil moisture over saturation at one day before mechanical testing. When measured, due to the limited space, all leaves of sample plants are removed in order to improve the measurement accuracy. The defoliated stalks were immobilized by a pair of lengthwise steel clamps to prevent stalks from bending (Fig. 7). After the digital pole dynamometer18 with a 1.5 m long slider and a main unit was linked to the stalks at a height of 80 cm away from the ground, the operator by hand pulled at a slow and uniform speed until the roots were pulled out. Records of load force, declination angle and sensor position were automatically stored in main unit during this operation. The peak value of forces, extracted from records, was taken as the max root side-pulling resistance.Figure 7Schematic diagram for measuring max root side-pulling resistance.Full size imageRoot anti-lodging indexBased on the method of Cui et al.6, the force value comparison is changed to the moment value comparison to calculate root anti-lodging index:$${text{AL}}_{root} = M_{root} / , M_{wind} = F_{root} / , F_{wind}$$
(1)
where M root is the root failure moment, M wind is the wind resultant moment. Root anti-lodging index indicates the ability of plants to resist root lodging. The larger its value is, the stronger the resistance is, and vice versa.$${text{M}}_{root} = F , *d$$
(2)
where F is the max root side-pulling resistance, d is moment arm, i.e., the length of force arm. As a component of root anti-lodging index, the root failure moment represents the ability of the root system to resist lateral pulling. The greater its value is, the better the resistance is, and vice versa.With the base of the stem as the fulcrum,$${text{M}}_{wind} = sum 0.{5}CA_{i} rho V^{2} h_{i}$$
(3)
where C is coefficient of air resistance, ρ is air mass density ,V is the wind speed , Ai is the area of a single leaf , hi is the height of leaf, ∑ represents to sum up over all leaves. C value is set to be 0.219. When encountering wind speed at grade 6 or higher, maize is more prone to lodging. Unless stated explicitly, the following analysis was limited to the upper wind speed for grade 6 wind20.Root morphological traitsThe number and length of all primary nodal roots were measured. Root-soil balls each of two or three tested plants were obtained after lateral root-pulling testing. The images of the three frontal sides, 120 degrees apart from each other, of the root-soil balls were taken using a digital camera. Ball volumes were then evaluated by considering them to be rotationally symmetric. Average volumes were used for further analysis.Single root tensile resistanceRoots after counting the number of nodal roots were used to measure the single root tensile resistance. First, clean the dust off roots. Then, diameters of roots were determined with a vernier caliper. Single root tensile resistance was measured by HF-500 digital push–pull apparatus. Fixed the upper and lower ends of the root, then one end moved slowly and uniformly, the other end was still until the root breaks. The peak tension force displayed by the instrument was taken as the single root tensile resistance.Statistical analysisBased on variance analysis, the Tukey method was used to compare the differences among means. The logarithmic transformation of variables was carried out to improve the homogeneity of error variance if appropriate.The substantive effect or influence of various factors on the response variable can be expressed by effect size of factors, which can be calculated under the framework of variance analysis. Effect size is the proportion of the effect of a certain factor in the total effect, which is a dimensionless number21,22,23.The formula for calculating effect size of factors is:$$omega^{2} = frac{{df_{effect} times left( {MS_{effect} – MS_{error} } right)}}{{SS_{total} + MS_{error} }}$$
(4)
where df is the degree of freedom, MS represents mean square.Two conceptual models were used when dealing with effect size. One model was of components, i.e., taking the logarithm of both sides of Eq. (1):$${text{LOG}}left( {{text{AL}}_{{{text{root}}}} } right) , = {text{ LOG}}left( {{text{M}}_{{{text{root}}}} } right) , + {text{ LOG}}left( {{text{M}}_{{{text{wind}}}} } right)$$
(5)
where LOG denotes logarithmic transformation.The other was the factorial model, i.e.,$${text{factors affecting AL}}_{{{text{root}}}} = {text{ wind grade }} + {text{ cultivar }} + {text{ growth stage}}$$
(6)
Experimental research and field studies on plants including the collection of plant materialThe authors declare that the cultivation of plants and carrying out study in Chengyang Agricultural Experimental Station complies with all relevant institutional, national and international guidelines and treaties.Statement of permissions and/or licenses for collection of plant or seed specimensThe authors declare that the seed specimens used in this study are publicly accessible seed materials and we were given explicit written permission to use them for this research. More

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Infection properties of clade A and clade B T7-like cyanophagesWe set out to test the hypothesis that the phylogenetic separation of T7-like cyanophages into two major clades reflects differences in their infection physiology. To do this we investigated a suite of infection properties of three pairs of clade A and B phages, each pair infecting the same Synechococcus host (Table 1) to allow us to control for variability in host genetics and physiology. These six cyanophages are representatives of 3 clade A and 2 clade B cyanophage subclades (SI Appendix, Table S1).Table 1 Summary of infection physiology of three pairs of clade A and clade B cyanophages infecting the same Synechococcus hosts.Full size tableWe began by investigating adsorption kinetics and the length of time taken to produce new phages in the infection cycle, the latent period, from phage growth curve experiments. In all three pairs of phages, adsorption was 7–15-fold more rapid in the clade A phage versus the clade B phage (Fig. 1, Table 1). Furthermore, the clade A phage had a faster infection cycle with a latent period that was 3-5-fold shorter than the clade B phage on the same host (Fig. 1a–c) (Table 1). To determine how representative these findings are for a greater diversity of T7-like cyanophages we report the latent period of nine additional non-paired phages that infect a variety of hosts and span the diversity of this cyanophage genus, measured here and taken from the literature (SI Appendix, Table S1). These phages showed the same pattern as observed between phage pairs, although one clade A phage had a relatively long latent period (see SI Appendix, Table S1). Overall, the 5 clade A phages representative of 5 subclades had a significantly shorter latent period (3.3 ± 3.6 h, n = 5 phages (mean ± SD) than the 10 clade B phages from 7 subclades (7.7 ± 2.0 h, n = 10 phages) (Kruskal-Wallis: χ2 = 4.72, df = 1; p = 0.029, n = 15). No significant differences in the length of the latent period were found for clade B phages that infected Synechococcus and Prochlorococcus (Kruskal-Wallis: χ2 = 1.13, df = 1; p = 0.29, n = 10).Fig. 1: Comparison of the infection physiology between pairs of clade A and clade B T7-like cyanophage infecting the same Synechococcus host.a–c Cyanophage growth curves, d–f burst sizes, g–i virulence as the percentage of lysed host cells, j–l decay as loss of infectivity, m–o plaque sizes. a, d, g, j, m Clade A Syn5 phage and clade B S-TIP37 phage infecting WH8109. b, e, h, k, n Clade A S-CBP42 phage and clade B S-RIP2 phage infecting WH7803. c, f, i, l, o Clade A S-TIP28 phage and clade B S-TIP67 phage infecting CC9605. The host strain is shown at the right of the panels. Red and blue lines or bars show results for clade A and clade B phages, respectively. a–c, g–I Error bars indicate standard deviations. d–f Burst size results are for single cells. j–l The solid line shows the fitted multi-level linear model. m–o The time after infection at which plaques were photographed appears above the images. *p value  More