Supplementary data of the review paper "Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes""

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Supplementary tables of the review paper "Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes". Supplementary Table 1. Characterised enzymes. Enzyme category: AT = acyltransferase, GT = Glycosyltransferase, HL = hydroxylase, MT = methyltransferase. Subcategory: SCPL = Serine carboxypeptidase-like, GT1 = Glycosyltransferase family 1, 2-ODD = 2-oxoglutarate-dependent dioxygenase, CYP450 = cytochrome P450, O-MT = O-methyltransferase. Supplementary Table 2. CYP450 enzyme families specificities of substrate and corresponding number of genes in Brassicaceae species. This table regroups and summarizes informations that have been found in "The Plant Cytochrome P450 Database" database (https://erda.dk/public/vgrid/PlantP450/table.html (Hansen et al. (2021), consulted in January 2023) and review articles from Xu et al. (2015) and Yu et al. (2017). The attribution of substrate specificities of CYP450 enzyme families was made according to the known substrate specificities of CYP450 enzyme members of each family. Hansen et al. (2021) - Molecular Plant, 2021, 14, 1244–1265 DOI: 10.1016/j.molp.2021.06.028 Xu et al. (2015) - Journal of Integrative Agriculture, 14(9): 1673–1686 DOI: 10.1016/S2095-3119(14)60980-1 Yu et al. (2017) - BMC Genomics, 18:733 DOI: 10.1186/s12864-017-4094-7 Supplementary Table 3. List of putative and characterised modification enzymes used for heatmap and phylogenetic tree analyses. Category: AT = acyltransferase, GT = Glycosyltransferase, HL = hydroxylase, MT = methyltransferase. Subcategory: GT1 = Glycosyltransferase family 1, 2-ODD = 2-oxoglutarate-dependent dioxygenase, CYP450 = cytochrome P450. Gene list accessions for each SM decoration enzyme category was established by combining key-word (e.g. “Hydroxylase”, “CYP450”, “2-oxoglutarate-dependent dioxygenase”, “SAM-dependent methyltransferase”, “O methyltransferase”, “Glycosyltransferase”, “Acyltransferase”, “SCPL”, “BAHD acyltransferase”)results research from The Arabidopsis Information Resource (TAIR - www.arabidopsis.org/), National Center for Biotechnology Information (NCBI, www.ncbi.nlm.nih.gov/) and the Carbohydrate-Active enZYmes (CAZy database - www.cazy.org; Drula et al., 2022) databases, together with lists found in Bontpart et al. 2015 (for acyltransferases) and Kawai et al. 2014 (for 2-oxoglutarate-dependent dioxygenases) Bontpart et al. (2015) - New Phytologist, 208(3):695-707. doi: 10.1111/nph.13498. Drula et al. (2022) - Nucleic Acids Research, 50(D1): D571–D577 doi.org/10.1093/nar/gkab1045 Kawai et al. (2014) - The Plant Journal, Apr;78(2):328-43. doi: 10.1111/tpj.12479. Supplementary Figure 1. Phylogenetic trees of A. thaliana enzymes putatively involved SM modifications. a) GT1 glycosyltransferases. b) O-methyltransferases. c) Acyltransferases. d) Hydroxylases. Different protein names are separated by slash. “*” means that the locus is expressed in seeds.  Enzyme amino acid sequences were retrieved from The Arabidopsis Information Resource (TAIR; https://www.arabidopsis.org/; genome release Araport11). Multiple alignments of Arabidopsis hydroxylases, methyltransferases, glycosyltransferases and acyltransferases (See Supplementary Table 2 for accessions list) sequences were performed using MUSCLE with default options (Edgar, 2004). The phylogenetic tree was inferred using the Neighbor-Joining (NJ). Bootstrap values were calculated for the highest iterations as possible (1000 for GT1 glycosyltransferases, 986 for methyltransferases, 284 for BAHD acyltransferases, 131 for SCPL acyltransferases, 760 for CYP450 hydroxylases and 993 for the rest of hydroxylases). The optimal trees are shown. Trees are drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic trees. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. All ambiguous positions were removed for each sequence pair (pairwise deletion option). Evolutionary analyses were conducted in MEGA11 (Tamura et al., 2021).