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Well this is my first guide ever! So if its kinda noobish then I am sorry.. This will not be the best Zyra guide right now maybe. but i played with this and i did good. I will be updating this guide as i find better things and combinations etc...

• Greater Mark of Magic Penetration is good rune for her because grant Magic Penetration which is very useful if using an AP Champion. Whether you like it or not Zyra is an AP user! Without Magic penetration then how will you get past those champions with Hight magic protection? exactly!
  
• Greater Seal of Scaling Mana Regeneration is good Seal to use because Zyra is a mana hungry in early game so having mana regeneration is good to help her farm those minions and harass those champions!
  
• Greater Glyph of Scaling Ability Power This is Very good Glyph for Zyra because this gives you more AP and since Zyra is an AP user this is a smart idea to get. This helps her Abilities do more damage.
  
• Greater Quintessence of Ability Power The reason i chose this was because it gives her some more AP for more damage to her doomed foes!

As always you should prioritize a champions ULT first.NO MATTER WHAT! So when you can, upgrade her Stranglethorns to give your plants increased attack speed, if in the area of effect, and to throw them into the air and stun them while at the same time doing a good chunk of damage to them.

I prioritized her Rampant Growth is because the less of a cool down you have on Rampant Growth then the more you can upgrade your Deadly Bloom, and Grasping Roots to help you get some good damage output on those doomed champions.

I found the second best thing to upgrade was Deadly Bloom so that you can put more damage and poke at those champions a little bit better.

The third prioritization was her Grasping Roots because they don't have the rang as Deadly Bloom and don't quite do as much damage but still an effective way to slow down enemy champions/ help you escape :)