It depends on the plant species and the contained phytochemicals.
I.e. for Hypericum I would use hypericin, hyperforin and phloroglucinols and flavonoids common in species of this genus. If you plan to analyse a Gentiana the choice may fall to secoiridoids (i.e gentiopicroside, swertiamarin) and xanthones.
The seroid diosgenin is the best known constituent of this species but also other classes of natural products have been identified such as saponins, phenolics (flavonoids, phenolic acids, diphenylethanoids, arylheptanoids, phenanthrene derivative, etc), diterpenoids. It depends also on the plant organs you want to analyse.
It is possible that several of these compounds are not commercial therefore you should purify them (and identifiy with suitable methods) to have the necessary standards. The following papers may be useful to have an idea about the phytochemicals contained in this apecies.
Tapondjou, L.A., et al., 2013. Steroidal saponins from the flowers of Dioscorea bulbifera var. sativa. Phytochemistry, 95, pp. 341-350.
Liu, H., et al., 2011. Phenolic compounds from the rhizomes of dioscorea bulbifera. Chemistry and Biodiversity, 8(11), pp. 2110-2116.
Kuete, V., et al., 2012. Antibacterial activities of the extracts, fractions and compounds from Dioscorea bulbifera. BMC Complementary and Alternative Medicine, 12,228.
Liu, H., et al., 2010. Norclerodane diterpenoids from rhizomes of Dioscorea bulbifera. Phytochemistry, 71(10), pp. 1174-1180.
Shi, W., et al., 2018. Metabolism of five diterpenoid lactones from: Dioscorea bulbifera tubers in zebrafish. RSC Advances, 8(14), pp. 7765-7773.
Secondary metabolites are diverse, it depend on what you are targeting. You need to do literature searching to find the most predominant compounds in the plant that you are working on. However, there are few metabolites that are common to many plants e.g Quercetin, Rutin, Gallic acid