You may not give your houseplants enough credit. What looks like an innocent philodendron gathering dust may actually be a riddle wrapped in a mystery shrouded in potting soil…at least genetically.

Turns out plants have some interesting genetic quirks that keep geneticists guessing. As challenges in finding gene-sequencing shortcuts, called barcodes, have made clear, deciphering plant genetics can be very tricky. Here's a roundup of five reasons plant DNA is totally confusing and totally fascinating to those who study it:

1- Enter the Cell: One unique feature of a plant cell is the chloroplast, the engine of photosynthesis. The DNA from chloroplasts is some of the most reliable in a plant cell. That's because it's inherited from only one parent, making it easier to understand than the DNA in the nucleus (more on that later!). However, there is a little catch: Occasionally chloroplasts can be transferred from one organism to another, even from one species to another. As a result, a plant's chloroplast may carry information totally unrelated to the species a geneticist is trying to study.

2- Tangled Family Trees: "A lot of plants are so long lived that they can do things we don't typically see in animals," says plant geneticist Damon Little of the New York Botanical Garden. "For example, you can have a mother tree reproducing with her great-grandson right beneath her." Plants overlap generations, travel minimally, and can clone themselves. They also mutate slowly. If genetic variation moves very slowly through a population, trees at one end of a forest can look different at the molecular level from trees at the other end, even though physically they are clearly the same species.

3- Two Genomes Are Better Than One: Plants have to withstand stressful conditions without the option of relocating. Fortunately, they've developed a handy trick to expand their adaptive repertoire: Pick up an extra genome. Through hybridization, organisms can double their genome, picking up additional sets of chromosomes. Animals with sex chromosomes—such as humans—are diploidic; they have two sets of chromosomes, one from each parent. Organisms with more than two sets are polyploidic. Wheat has 6 sets, 42 chromosomes total; coffee can have 8 sets of 11 chromosomes, or 88 total.* Many sets makes deciphering one or two markers in the tangled skein of chromosomes in a plant cell's nucleus a Sisyphean task.

4- Sometimes, One Genome Is Better Than Two: Given the stresses plants endure, they have all—at some point in their history—been polyploids. But that doesn't mean they stay that way. Over time, genes that confer no advantage are dropped. The process is sped up by the fact that an imbalance in genetic material creates new problems. In plants as in animals, an extra chromosome can have serious effects. Klinefelter's and Down's syndrome are human examples, and certain crop diseases are caused by the existence of an extra chromosome. As a result, plant species such as mace, which were polyploidic 10 million years ago, have cast off most of the extra genes they once had so that today they are nearly diploidic. "This makes these plants very confusing to analyze," says Luca Comai, a plant geneticist at the University of California Davis. Rice, for example, is a diploid plant today, but its genetic sequence still bears the fingerprints of polyploidy—traces of other genomes.

5- The Fungus among Us: "You don’t often think about this, but all of life as you know it is covered with fungi," Little says. Some plants are more prone to fungal contamination than others, and the result, according to Little, is that as many as a quarter of the plant samples in the genetic archive GenBank are actually fungal. Another common culprit of contamination is microbial DNA that slips into a sample. Fortunately, these kinds of contaminations can be corrected when savvy scientists spot irregularities. As more plants (and for that matter microbes and fungi) are examined, geneticists can catch and correct more contamination errors.

"Plant DNA can be more complicated because of the duplicity of its nature," Comai says. "You might look inside and find it closely resembles another plant. But you might be missing a whole other genome, and then it's a totally different critter." Duplicitous daffodils—who'd have thunk it?

* Correction (5/8/12): This sentence was edited after posting to correct the numbers of chromosomal sets given for wheat and coffee.