Dandelions in the city
In this time of year, the common dandelion— Taraxacum officinale — can be found almost everywhere. Their bright yellow flowers and fluffy seed heads are a common sight in lawns, gardens, and other green spaces. The mild temperatures and increased rainfall of spring provide ideal growing conditions for dandelions, allowing them to quickly reproduce and spread.
Dandelions are often considered a nuisance and are therefore disliked by many people. This is because they are highly invasive and can quickly take over lawns, gardens, and other green spaces. They reproduce rapidly and can spread through both their seeds and their long taproots, making them difficult to control. In addition, the bright yellow flowers of dandelions are often viewed as unsightly, and their fluffy seed heads can quickly spread throughout the surrounding area, further contributing to their invasive nature.
I never really understood this dislike of dandelions. They are an important source of nectar and pollen for bees and other pollinators, and their leaves can be used in salads or cooked as a vegetable, as they are rich in vitamins and minerals. Also, they have several amazing biological features that are described in the ~1,000 or so scientific articles about the dandelion genus Taraxacum. The fluffy, white “parachutes” that surround the seeds allow them to be carried great distances and colonize new areas by even the slightest breeze. They have a deep taproot system that can reach up to several meters underground, making them particularly drought-tolerant. They are also able to grow and reproduce at an incredibly fast rate, with some plants producing up to 15,000 seeds in a single growing season.
Perhaps, the most remarkable feature of dandelions is their ablility to reproduce asexually by producing clones of themselves through a process called apomixis, meaning asexual seed production. This means that a single dandelion plant can produce offspring without the need for pollination or sexual reproduction, allowing them to rapidly spread and colonize an area. Research on dandelion apomixis can have real world impact on agriculture. One goal would be to achieve synthetic apomixis in crops that do not carry this trait. In a recent study, Charles Underwood and colleagues at Keygene in Wageningen, The Netherlands, managed to get a gene from the apomictic dandelion to induce egg cell division without fertilization in lettuce, taking us a step closer to breeding apomictic crops.
Asterales everywhere!
Dandelions are in the flowering plants order of the Asterales that includes some of the most well-known and beloved species in the world. These plants are characterized by their composite flowers, which consist of many small individual flowers arranged in a head or cluster. The order includes over 25,000 species, ranging from sunflowers and daisies to chamomile and coneflowers. Many of these species are popular garden plants, valued for their attractive flowers, hardiness, and adaptability. The Asterales order plays an important ecological role, providing food and habitat for many species of insects, birds, and other animals. In spring, I love spotting beetles on the bright yellow flowers of Asterales. Check this video I took in Tabarka, Tunisia, in April 2022 of Paratriodonta scarab beetles frolicking and fighting on a flower of the Asterales Picris hieracioides.
Do you know what I hate? It’s not the dandelions. What I hate is roadside mowing. We keep hearing about the insect apocalypse and how insects are disappearing at an alarming rate. Yet, we continue the useless tradition of mowing the wildflowers and plants that line our roads and highways. And with the plants go all the insects and other animals that depend on them.
Lactuca is another genus of plants in the Asterales order. If you maintain a healthy diet, chances are that you consume Lactuca spp. daily, as the common salad lettuce ingredient. This is the genus includes many species of lettuce, including Lactuca sativa, which is the most commonly cultivated lettuce species. Lettuce breeding is a fascinating and complex activity that has yielded an incredible diversity of lettuce cultivars. Beneficial genes that end up in the many lettuce varieties on our supermarket shelves are drawn from over a dozen of Lactuca species. This includes anything from genes that confer disease resistance to those that improve shelf life.
This goes to show how diverse dandelions and their relatives can be. They are living organisms that are critical for the advancement of scientific research and our food security. We depend on them for a healthy diet and as a source of food. This warehouse at the De Lier headquarters of the Dutch vegetable seeds company Rijk Zwaan holds a significant fraction of the world’s seed collection for crops like lettuce and other vegetables. Standing there in the midst of all those bags of seeds, I couldn’t help but feel grateful for the genetic diversity that plant breeders have harnessed for the benefit of humanity.
Dandelion and immune receptor repertoires
My laboratory became interested in the asterid clade of flowering plants , which includes the Asterales, after my PhD student Chih-hang Wu and teammates discovered in the mid-2010s that a large number of immune receptors in the NLR class form networks. He traced back the emergence of this receptor network to about 100 million years ago, early in the evolution of asterids. This discovery has had a huge impact on my lab’s research as it inspired us to pivot to studying NLR biology and evolution. Chih-hang also continues to study NLR networks in his own lab at Academia Sinica, Taipei, Taiwan. At a recent meeting in Tuebingen, Germany, he explained how some asterid species have up to 80% of their immune receptors in the NLR network he discovered.
Our interest in the diversity of immune receptors of asterids, Asterales, dandelions and related species is why the title of this paper immediately caught my attention. At first glance, what do you make of this?
The paper has absolutely nothing to do with the amazing dandelion plant. The authors developed a bioinformatics tool that they elected to name Dandelion and further they decided to highlight the ambiguous name in the title of their paper.
My first reaction was to view this as another case of plant blindness. Yet another example of the tendency to ignore the importance of plants in human affairs. Plant blindness also affects scientists, notably our biomedical colleagues, who sometimes forget that plants are actually living organisms with their own biological features. In one famous anecdote, a biomed colleague exclaimed “it’s alive!” after viewing a video of a Mimosa leaf shutting down after being touched.
But as the Twittersphere was quick to remind me, the affliction of naming bioinformatics stuff after living organisms is a common practice that goes beyond borrowing plant names. rens holmer (no Capitals), on the top of his head, listed: Guppy, Pandas, Polars, Taxus, Picea, Caretta. Mark Zieman revealed that Salmon — a tool for quantification of transcript expression — has received over 5,000 citations. And of course, there is the programming language Python as pointed out by Shyam Singh Solanki.
All of this doesn’t make me feel any better about the practice. We name things to communicate clearly and unambiguousy. Naming bioinformatics tools after organisms is unhelpful and confusing. And just because something is fashionable and popular at some point doesn’t mean that it should stick with us forever. Remember saggy pants?
You say tomato, I say it shouldn’t be a protein name
If you thought the problem of naming things after plants and other organisms was limited to computational pipelines, think again. This practice extends to genes and proteins as well. I can live with Time for Coffee, the Arabidopsis circadian clock regulator better known at TOC. I can tolerate Homo sapiens hepatocyte odd protein shuttling protein or HOPS — no relation to the Cannabaceae hop plant Humulus lupulus that flavours your beer. But for years we’ve used the red fluorescent protein known as tdTomato. And we work on Phytophthora infestans, a pathogen of tomato, and used transformants of this microbe that express tdTomato, which means that all these years we’ve been writing papers on infecting tomato with a tomato pathogen that expresses tdTomato. In some studies, such as this one, we did our best to avoid writing tdTomato, introducing it just once. But sometimes, it’s harder to avoid this as in this paper from our plant pathologist colleagues who studied the tomato bacterial pathogen Candidatus Liberibacter solanacearum.
It may seem evident that a bright variant of the red fluorescent protein was named after the tomato plant to reflect its red color, but I can’t help but feel that whoever came up with such an unoriginal name never bothered to think that tomato scientists would use their fluorescent marker. Call me sensitive if you like, but to me this has plant blindness written all over it.
Stop naming biological tools and material after living organisms
I was surprised to see a tweet from Rob Patro, the author of Salmon (the software), stating that ‘naming software is hard!’ I find this hard to believe. It seems puzzling that creative people who can write complex computational pipelines and invent new proteins cannot come up with any other names than plants and animals.
How about naming things after movie characters, historical figures, unusual objects etc. If you’re really stuck, I recommend Bozo (as in The Clown) or NEMO (instead of Salmon). And what about Droop, Slouch, Dangle, Sag, Hang. These are all one word names suggested by ChatGPT as being inspired from the once fashionable saggy pants.
And there is always the overlooked Random Name Generator. Check it out, dear colleagues.
But, whatever you do, please stop naming your biotools and biomaterial after living organisms, especially plants. I know some think it’s cute and original, but please stop.
Acknowledgements
This post was written with assistance from ChatGPT.
This article is available on a CC-BY license via Zenodo. Cite as: Kamoun, S. (2023) Dandelion and tdTomato: Stop naming bioinformatics tools and biomaterial after living organisms. https://doi.org/10.5281/zenodo.7843514
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