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When creating the plant life on alien planets, photosynthetic pigments other than chlorophyll can be the predominant molecule to create foliage of colours other than green, as we see on earth but for the minority of plants. But most trees and woody plants have brown bark, other than the few examples like silver birch which has light coloured bark to regulate its temperature.

Some plants have green bark as chlorophyll is present but they are in the minority, although if other photosynthetic pigments are present in the leaves the bark could be that colour but as the majority of plants have brown bark you could assume that on alien planets not all bark will contain photosynthetic pigments so some sort of other coloured bark will likely be present.

Tannins are the molecule in woody bark responsible for giving the brown colour and its purpose is to protect the plant from pest. This makes me wonder if other molecules could replace tannins to carry out the same functions for the plant but would give the bark another colour other than brown?

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Metal salts and chelates.

nickel sap

https://www.ausimm.com/bulletin/bulletin-articles/growing-nickel-from-trees/

Some of the most colorful molecules in nature are metal chelates. Depicted: sap from a nickel hyperaccumulator. I had not seen this vivid green which looks more like an iron salt. Other famous colorful metal chelates include hemoglobin, hemocyanin, cyanocobalamin and so on. Tunicates use vanadium defensively which gives those organisms an awesome purple color.

tunicates with vanadium

https://quantumbiologist.wordpress.com/2011/06/22/v-for-vanadium/

Your alien trees bioaccumulate metals and chelate them in the bark and sap. This fulfulls your request that the color of the bark be related to the biologic defenses of the plant.

Of course you can get colorful bark without all that. The rainbow eucalyptus has the most colorful bark of any tree, just because it is living its own 250 foot tall colorful truth.

rainbow eucalyptus

https://www.australiangeographic.com.au/topics/science-environment/2019/07/who-painted-the-bark-meet-the-magnificent-rainbow-eucalyptus/

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    $\begingroup$ It would be fun to have a rainbow eucalyptus in my yard here in Florida. $\endgroup$
    – FlaStorm32
    May 23 at 0:04
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    $\begingroup$ @FlaStorm32 Provided nothing ever happens that causes it to catch fire. Eucalyptus trees are a serious fire hazard because the oil and sap are extremely flammable, and burning eucalyptus has a tendency to literally explode. $\endgroup$ May 23 at 14:06
  • $\begingroup$ Also check Federal, state, and local laws; it's possible that might be classified as a "noxious" or "invasive" species on the opposite side of the Earth from its native land. $\endgroup$
    – Zeiss Ikon
    May 23 at 14:21
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Some plants also produce alkaloids to get protection from pests:

Most of the known functions of alkaloids are related to protection. For example, aporphine alkaloid liriodenine produced by the tulip tree protects it from parasitic mushrooms. In addition, the presence of alkaloids in the plant prevents insects and chordate animals from eating it.

Then of course there are exception like us humans growing coffee for the alkaloid caffeine contained into it, not mentioning other less legal alkaloids.

In any case, also this substances are not that much different in color from tannin, as far as I know.

If there is no need for a specific color selection, there is no driving force for evolution to select it.

If you want colored bark, maybe you can make use of interference patterns in the bark, so that they can display iridescent colors like the feathers of some birds or the wings of butterflies.

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Frame challenge

You can make the bark any color you want, because you’re already dealing with different biochemistries.

Put simply, the compounds produced by plants to stop pests are generally only toxic when considered in the context of specific biochemistries.

You can see this on Earth IRL. Examples off the top of my head include:

  • Capsaicin makes chili peppers spicy for many mammals, but many birds are unaffected by it.
  • Allium species (garlic, onion, chives, leeks) are toxic to most canids and felids, but not to humans.
  • Horseradish, mustard, wasabi, and a whole slew of similar plants are toxic to horses, but not to humans.
  • Many alkaloids are very effective protection against small animals, but not so much against humans, and there are often specific species that are unaffected by them.

There’s no reason though that your alien trees would need to protect against pests from Earth, so there’s no reason that whatever they have in their bark has to be toxic against typical terrestrial biochemistries. The fact that you are assuming things are alien therefore means you can just state that some specific compound which gives the tree bark an interesting color happens to be mildly toxic to pests native to that planet.

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    $\begingroup$ That means you could have bark colored with orange β-carotene (like in carrots), red betanin (as in beetroot), pelargonidin (rose to red, present in strawberries) or even why not purple permanganate ions. You just need pests for which these molecules are toxic. $\endgroup$
    – Axel B
    May 23 at 18:56

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