Pisum sativum

Several sequence resources were combined, forming a custom, redundant protein database. Expressed Sequence Tags (EST) databases from A. thaliana (release 12.1), Brassica napus (release 1), C. reinhardtii (release 5), G. max (release 10), Lotus japonicus (release 3), Lycopersicum esculentum (release 10.1), M. truncatula (release 8), Nicotiana tabacum (release 2), O. sativa (release 16), Solanum tuberosum (release 10), and Z. mays (release 16) were downloaded from the TIGR Gene Indices (now available at the Dana-Farber Cancer Institute gene index project) [49 (link)]. TIGR Transcript Assemblies (TA) from A. thaliana, Brassica napus, C. reinhardtii, P. patens, G. max, Glycine soja, Lotus corniculatus, Lupinus albus, Lycopersicum esculentum, M. sativa, M. truncatula, Nicotiana tabacum, O. sativa, Phaseolus coccineus, Phaseolus vulgaris, Pisum sativum, Solanum tuberosum, and Z. mays were added to this set (all release 1, 15 August 2005) [50 (link)]. The proteins predicted from the plant genomes of A. thaliana (NCBI Genbank release 5, 03 May 2006) [57 (link)], C. reinhardtii (JGI, release 3) [58 (link)], M. truncatula (Genome Sequencing Project release 17 July 2006) [59 (link)], O. sativa (release 4, 30 December 2005) [60 (link)], and P. trichocarpa (JGI, release 1) [61 (link)] were also included.
Sequence names were truncated to a unique identifier. Information about the database origin of each sequence was added to the unique identifier (i.e. OS-TA, OSEST, OSGEN for O. sativa TA, EST or genomic sequences respectively). Nucleotide sequences were translated into protein sequences in all six reading frames (universal code), and frame information was appended to the sequence identifier (e.g. "_+2"). The translated nucleotide sequences and modified protein sequences derived from genomic data were combined into a single file and formatted using Formatdb (options: -p T and -o T) [43 (link)]. The resulting database contained 3,631,558 sequences. To determine whether CLE sequences were specific to plants, a separate search was based on the non-redundant protein database (NCBI nr, version 15 June 2006.).

The atomic coordinates were taken from the X-ray structures; cyanobacterial PSI from Thermosynechococcus elongatus at 2.5 Å resolution (PDB code, ; 1JB0);2 (link) plant PSI from Pisum sativum at 2.8 Å resolution (PDB code, ; 4XK8); PbRC from Rhodobacter sphaeroides at 2.01 Å resolution (PDB code, ; 3I4D), 1.87 Å resolution (PDB code, ; 2J8C),4 (link) and 2.55 Å resolution (PDB code, ; 1M3X);3 (link) PbRC from Thermochromatium tepidum at 2.2 Å resolution (PDB code, ; 1EYS);30 (link) the PSII monomer unit (designated monomer A) of the PSII complexes from Thermosynechococcus vulcanus at 1.9 Å resolution (PDB code, ; 3ARC).5 (link) Hydrogen atoms were generated and energetically optimized with CHARMM.54 Atomic partial charges of the amino acids were adopted from the all-atom CHARMM22) parameter set.55 (link) For PSI, the atomic charges of cofactors were taken from previous studies (Chla, phylloquinone, β-carotene,56 (link) and the Fe₄S₄ cluster57 ). The atomic charges of the other cofactors ((B)Chla, including (B)Chla˙⁺ and (B)Chla˙^–, (B)Pheoa, ubiquinone, plastoquinone, spheroidene, sulfoquinovosyl diacylglycerol, heptyl 1-thiohexopyranoside, and the Fe complex) were determined by fitting the electrostatic potential in the neighborhood of these molecules using the RESP procedure58 (Tables S2–S11†). To obtain the atomic charges of the Mn₄CaO₅ cluster or the Fe complex, backbone atoms are not included in the RESP procedure (except for D1-Ala344) (Table S11†). The electronic wave functions were calculated after geometry optimization by the DFT method with the B3LYP functional and 6-31G** basis sets, using the JAGUAR program.59 For the atomic charges of the non-polar CH_n groups in cofactors (e.g., the phytol chains of (B)Chla and (B)Pheoa and the isoprene side-chains of quinones), the value of +0.09 was assigned for non-polar H atoms. We considered the Mn₄CaO₅ cluster to be fully deprotonated in S₁.
The protein inner spaces were represented implicitly with the dielectric constant ε_w = 80, whereas the following water molecules were represented explicitly; (i) for PSII, ligand water molecules of the Mn₄CaO₅ cluster (W1 to W4), a diamond-shaped cluster of water molecules near TyrZ (W5 to W7)60 (link), the water molecule distal to TyrD44 (link), ligand water molecules of Chl_D1 (A1003 and D424), Chl_D2 (A1009 and A359), and other Chla (B1001, B1007, B1027, C816, and C1004); (ii) for PSI, clusters of water molecules near A_1A (A5007, A5015, A5022, A5043, and A5049) and A_1B (B5018, B5019, B5030, B5055, B5056, and B5058), ligand water molecules of A_–1A (B5005), A_–1B (A5005), and other Chla (A5004, A5010, A5012, A5024, A5032, A5051, B5006, B5010, B5022, B5036, B5053, B5054, J127, L4023, and M155).

Field tests and soil, plant and entomological sampling were carried out in 2018–2020, at the beginning of June in the flag leaf stage of spring wheat (BBCH 39). The research was conducted on spring wheat grown in OPS and CPS. The experimental factors were: factor Ix—spring wheat species (Fig. 1); Indian dwarf wheat (Triticum sphaerococcum Percival) and Persian wheat (Triticum persicum Vavilov); factor II—sowing density 400, 500, 600 (seeds m). The experiments were performed in a split-plot arrangement in four replicates. The single plot size of 21 m². Triticum sphaerococcum Percival cv. Trispa and Triticum persicum Vavilov cv. Persa used in our field experiments are the cultivars, which has been bred by the Bydgoszcz University of Science and Technology in 2020. The Breeder’s Right, granted by the director of Research Centre for Cultivar Testing, is exercisable on the territory of Poland at the national Plant Breeders’ Rights protection level. Details on soil characteristics prior to the experiments can be found in Lemanowicz et al. (2020a) (link) and Lemanowicz et al. (2020b) (link). The forecrops for the tested species of OPS and CPS cultivated spring wheats were cereals (triticale or winter wheat). Immediately after harvesting the forecrop, an intercrop of peas of the tendril-leaved variety ‘Tarchalska’ were sown at a rate of 240 kg ha¹. Pre-winter ploughing was carried out to a depth of 0.22–0.23 m. Sowing parameters, as well as methods of fertilization and plant protection against weeds, diseases and pests were provided by Lemanowicz et al. (2020a) (link) and Lemanowicz et al. (2020b) (link).

A total of 32 snow peas (Pisum sativum var. Saccharum cv Carouby de Maussane) were chosen as study plants. For each pot, 6 seedlings were potted at 8 cm from the pot’s border and sowed at a depth of 2.5 cm. Once germinated, one healthy-looking sprout was selected and randomly assigned to the experimental conditions: 19 plants were grown individually in chambers without the presence of a support (“no support” condition; Figure 1a), while 13 plants were grown individually in chambers where a potential support was present (“support” condition; Figure 1b). Sprouts were placed 8 cm from the pot’s border and sowed at a depth of 2.5 cm. The support was a wooden pole (54 cm in height and 1.3 cm in diameter) inserted 7 cm below the soil surface and positioned 12 cm away from the plant’s first unifoliate leaf.

Virtual RFLP patterns were generated by in silico digestion of the 1.2 kb DNA fragment (R16F2n/R16R2) of the 16S rRNA gene identified from Pisum sativum witches’ broom phytoplasma (accession No. OM827254) and Parthenium hysteroporus witches’ broom phytoplasma (accession No. OM215201) using iPhyClassifier, an interactive online tool (https://plantpathology.ba.ars.usda.gov/cgi-bin/resource/iphyclassifier.cgi, accessed on 1 April 2022) [42 ].