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You need to put fungs that closely match those colors into those slots. So a gate can only be made with a GREEN fung, a YELLOW fung, and two fiberoyd boards (fences). If you can't find any fungs that match those colors, you will have to wait until some evolve, or try breeding some!

how do i breed plants? i didnt know i could do that!

All of the life forms in Vilmonic reproduce asexually, so to create different breeds you will need to propagate those that have the traits you are looking for. To breed yellow fungs you will have to pick the yellowest of your green fungs and plant them around, continually picking and planting the yellowest of each generation until you finally have yellow fungs. This is essentially artificial selection. You can use a similar technique to generate any color fung. Their colors migrate based on the colors of the rainbow, so red becomes orange becomes yellow - green - blue - purple (indigo) - and back to red.