Category Archives: Molecular Biology

You know nothing, humans! A planarian genome challenges our understanding of how life works

by Piter Kehoma Boll

We finally have a rather complete sequencing of a planarian’s genome, more precisely, of the planarian Schmidtea mediterranea, which is an important model organism for the study of stem cells and regeneration.

In case you don’t know, planarians have a remarkable ability of regeneration, so that even tiny pieces are able to regenerate into a whole organism. They are like a real-life Wolverine, but somewhat cooler! This amazing ability is possible due to the presence of a group of stem cells called neoblasts that can differentiate into any cell type found in the planarian’s body. In fact, all differentiated cell types in planarians are unable to undergo mitosis, so that neoblasts are responsible for constantly replacing cells in every tissue. But we are not here to explain the details of planarian regeneration. We are here to talk about Schmidtea mediterranea‘s genome!


Look at its little cock eyes saying “I will destroy everything you think you know, humans!” Photo by Alejandro Sánchez Alvarado.*

A rather complete genome of S. mediterranea has been recently published and its analysis reveal some astonishing features.

First of all, 61.7% of S. mediterranea‘s genome is formed by repeated elements. Repeated elements are basically DNA strands that occur in multiple copies throught the genome of an organism. They are thought to come from the DNA of virus that was incorporated to the host’s DNA. In humans, about 46% of the genome is formed by repeated elements. Most repeated elements of S. mediterranea belong to unidentified families of retroelements, thus suggesting that they are new undescribed families. Those repeats are very long, having more than 30 thousand base pairs, which are not known to exist in other animals. The only other group of repeated elements with a similar size is found in plants and known as OGRE (Origin G-Rich Repeated Elements). The long repeat found in Schmidtea was therefore called Burro (Big, unknown repeat rivaling Ogre).

But certainly the most surprising thing about S. mediterranea‘s genome is the lack of many highly conserved genes that are found in most eukaryotes and that were thought to be essential for cells to function properly.

Schmidtea mediterranea lacks genes responsible for repairing double-stranded breaks (DSBs) in DNA, which would make them very likely to suffer a lot of mutations and sensitive to anything that induces DSBs. However, planarians are known to have an extraordinary resistance to gamma radiation that induces DSBs. Do they have other repairing mechanisms or is our current understanding about this process flawed?


Several “essential” genes and their presence (in green) or absence (in red) in several animals. Schmidtea mediterranea lacks them all. Image extracted from Grohme et al. (2018).**

Another important gene that was not found in S. mediterranea is the Fatty Acid Synthase (FASN) gene, which is essential for an organism to synthesize new fatty acids. Planarians therefore would have to rely on the lipids acquired from the diet. This gene is also absent in parasitic flatworms and was at first thought to be an adaptation to parasitism but since it is absent in free-living species as well, it does not seem to be the case. Could it be a synapomorphy of flatworms, i.e., a character that identifies this clade of animals?

That is not enough for little Schmidtea, though. More than that, this lovely planarian seems to lack the MAD1 and MAD2 genes, which are found in virtually all eukaryotes. Those genes are responsible for the Spindle Assembly Checkpoint (SAC), an important step during cell division that prevents the two copies of a chromosome to separate from each other before they are all connected to the spindle apparatus. This assures that the chromosomes will be evenly distributed in both daughter cells. Errors in this process lead to aneuploidy (the wrong number of chromosomes in each daughter cell), which is the cause of some genetic disorders such as the Down syndrome in humans. Planarians do not have any trouble in distributing their chromosomes properly, so what is going on? Have they developed a new way to prevent cellular chaos or, again, is our current understanding about this process flawed?

Let’s wait for the next chapters.

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Grohme, M. A.; Schloissnig, S.; Rozanski, A.; Pippel, M.; Young, G. R.; Winkler, S.; Brandl, H.; Henry, I.; Dahl, A.; Powell, S.; Hiller, M.; Myers, E.; Rink, J. C. (2018). “The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms”. Nature. doi:10.1038/nature25473

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Friday Fellow: Spreading Earthmoss

by Piter Kehoma Boll

If you still think mosses are uninteresting lifeforms, perhaps you will change your mind after knowing the spreading earthmoss, Physcomitrella patens.

Found in temperate regions of the world, except for South America, but more commonly recorded in North America and Eurasia, the spreading earthmoss grows near water bodies, being one of the first species to colonize the exposed soil around pools of water. Although widely distributed, it is not a common species.


The spreading earthmoss growing on mud. Photo by Hermann Schachner.

Since the beginning of the 1970s, the spreading earthmoss has been used as a model organism, especially regarding gene manipulation. Differently from what occurs in vascular plants, the dominant life phase in mosses is the gametophyte, an haploid organism, meaning it has only one copy of each chromosome in its cells. This is an ideal condition for the study of gene expression, as the activation or inactivation of a gene is not hindered by a second one in another copy of the chromosome in the same cell.


Physcomitrella patens growing in the lab. Credits to the Lab of Ralf Reski.*

By controlling gene expression in the spreading earthmoss, researches can track the role of each one of them in the plant’s development. Comparing these data with that known from flowering plants, we can have a better understanding of how the plant kingdom evolved.

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Cove, D. (2005). The Moss Physcomitrella patens Annual Review of Genetics, 39 (1), 339-358 DOI: 10.1146/annurev.genet.39.073003.110214

Schaefer, D. (2001). The Moss Physcomitrella patens, Now and Then PLANT PHYSIOLOGY, 127 (4), 1430-1438 DOI: 10.1104/pp.127.4.1430

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The fabulous taxonomic adventure of the genus Geoplana

by Piter Kehoma Boll

Freshwater planarians are relatively well-known as those cute arrow-shaped cockeyed animals. Land planarians are far away from having all the fame of their aquatic cousins and most people do not even know that they exist. Maybe in part it is because deeper studies of the natural world began in Europe, a continent were land planarians are almost non-existent. The first of those little animals to be known was described in 1774 by the Danish naturalist Otto Friedrich Müller. He named the small worm Fasciola terrestris, because he thought it was a terrestrial version of the parasitic worm. It was a small cyllindrical worm with a dark back and two small eyes at the anterior region.


In 1788, the naturalist Johann Friedrich Gmelin transfered the species to the genus Planaria, described in 1776 by Müller. The worm was, therefore, now called Planaria terrestris. The genus, at this time, included everything that is currently known as planarian: worms with a ventrally located mouth, close to the middle part of the bod. The term most likely became popular by this time and so it continues until today as a general name for these animals.



Planarians with many eyes were transfered in 1831 by the naturalist Christian Gottfried Ehrenberg to a new genus, Polycelis. The term means “many dots” and refers to the dark dots that the eyes represent on the body.



During Charles Darwin’s voyage around the world aboard the Beagle, he spent some time in the Brazilian Atlantic Forest and found several species of land planarians. He classified them in the genus Planaria, but highlighted that they formed a section within the genus because of their terrestrial habits, convex bodies and often colorful stripes. The first new species listed by him was called Planaria vaginuloides and was collected in the forests of Rio de Janeiro. The epithet vaginuloides was chosen because Darwin found them to be similar to slugs of the genus Vaginulus.



One year later, in 1845, the naturalist Émil Blanchard found a species in Chile and named it Polycladus gayi. The name of the genus, Polycladus, refers to the highly branched gut of these animals, while the epithet gayi honors the naturalist Claudio Gay. But Blanchard made a terrible mistake: he mistook the anterior end for the posterior end and so thought that the genital opening was in front of the mouth!



In 1850, the naturalist Karl Moriz Diesing transferred Darwin’s land planarians to the genus Polycelis because they have many eyes. Planaria vaginuloides was now Polycelis vaginuloides.



In 18851, the zoologist Joseph Leidy found another land planarian species in Europe that was also small, cylindrical and with two eyes. He named it Rhynchodemus sylvaticus. The term Rhynchodemus means something like “bill-shaped body”. He also suggested the transference of Planaria terrestris to the new genus, so that it was now Rhynchodemus terrestris. Darwin and Blanchard’s species remained as Polycelis and Polycladus.



Then in 1857 something funny happened. A new revision of land planarians was done by William Stimpson. He, for the first time, separated land planarians from freshwater ones and divided them in two families:

  1. Polycladidae: having a single genus, Polycladus, because it was still thought, at this time, that the genital opening was before the mouth.
  2. Geoplanidae: the rest of land planarians. Species in this family were divided into three genera:
  • Rhynchodemus: species with two eyes;
  • Bipalium: a genus for recently discovered species that have a hammer- or crescent-shaped head. The name comes from Latin bi-, two and pala, shovel.
  • Geoplana: species with many eyes. The name comes from geo, earth, and plana, flat, because of the flat body of those animals, as well as a direct reference to the genus Planaria, now restricted to aquatic species. The species Polycelis vaginuloides became Geoplana vaginuloides. So we arrive to the central genus of this story.


By a huge coincidence, in this very same year of 1857, the naturalist Max Schultze, based on information from literature and new species collected in Brazil by the naturalist Fritz Müller, also decided to separate land planarians into another genus and also chose the name Geoplana! What are the chances? The papers of Stimpson and Schultze had only some weeks between them and everything seems to indicate that Schultze was unaware of Stimpson’s paper. The main difference between both papers is that Schultze ignored the discovery of the species classified as Bipalium. He also transfered all land planarians to Geoplana, so that Polycladus gayi, Rhynchodemus sylvaticus and Rhynchodemus terrestris were now Geoplana gayi, Geoplana sylvatica and Geoplana terrestris.



Stimpson’s system, however, prevailed, and the four genera remained in use: Rhynchodemus, Bipalium, Geoplana and Polycladus. Among the species described by Schultze and Müller was Geoplana subterranea, an albine and eyeless species found underground and that feeds on earthworms. In 1861, Diesing decided to put this species into its own genus, Geobia. We had now 5 genera: Rhynchodemus, Bipalium, Geoplana, Geobia and Polycladus.



In 1877, Henry Nottidge Moseley described a series of species from Australia, the Pacific and southeast Asia. A good amount of them were included in the genus Geoplana, but some of them were put in two new genera:

  1. Dolichoplana (“long flat”): very long and narrow species with two eyes as in Rhynchodemus;
  2. Caenoplana (“recent flat”): species considered by him to be intermediate between Geoplana and Dolichoplana because the body was longer and the eyes were restricted to the sides of the body.


Ten years later, in 1887, J. J. Fletcher and A. G. Hamilton studied Australian land planarians and concluded that there was no need for the species named Caenoplana by MOseley to be in a separate genus and united them to Geoplana.



During the following decade, the naturalist Arthur Dendy described several new species from Australia and New Zealand, classifying all in the genus Geoplana. The genus was growing, having tenths of species. In the last years of the 19th century, several new genera were created, many of them in the works of the zoologist Ludwig von Graff. These new genera were erected to species with very peculiar anatomical features, such as a differentiated head, for example. Anyway, the genus Geoplana kept growing. Any flat and many-eyed land planarian without a distinct feature was thrown into this genus. This system continued throughout most of the 20th century. Tenths of new species were described by the zoologist Libbie Hyman and by two zoologist couples: the Marcuses – Ernst Marcus and Eveline du Bois-Reymond Marcus – and the Froehlichs — Claudio Gilberto Froehlich and Eudóxia Maria Froehlich. These new species were mostly put in Geoplana. At that time the genus was widely distributed in South America and Australia.



During this time, E. M. Froehlich determined that Geoplana vaginuloides should be the type species of the genus Geoplana. Perhaps you are now asking yourself “what is a type species?”. Well, in taxonomy, when a new genus is created, one of its species has to be considered the type species, the species that serves as a “model” to the genus. It is the type species that defines what the genus is. Once a species becomes the type species of the genus, it can never pass to another genus, except if the entire genus ceases to exist. Afterall, it is the species in which the existence of the genus is based. The fact is that in the 18th and 19th centuries there was no policy of type species, which was only later introduced in the rules to give names to organisms. Therefore Stimpson, when he created the genus Geoplana, did not define a type speciees. E. M. Froehlich chose Geoplana vaginuloides as the type-species because it was the first species listed by Stimpson and the proposal was accepted by the scientific community.

Let’s go back to the main subject. As it was said, the genus Geoplana was gathering more and more species throughout the 20th century, becoming huge. Then in 1990 the zoologists Robert Ogren and Masaharu Kawakatsu decided to clean the mess. By examining the inner anatomy of land planarians, they excluded from Geoplana all species from Australia and nearby areas because they have testes placed in the ventral region of the body, diferently from South American species, that have them in the dorsal region. However, letting all the South American pack inside Geoplana would still be a mess. So, they broke the genus into several smaller genera. The four main genera were defined based on two features of the copulatory apparatus: 1) the presence or absence of a penis papilla, i.e., a penis. Some planarians have a penis and some don’t. 2) The position of the oviducts, i.e., the canals that carry the eggs from the ovaries to a cavity named female atrium. The oviducts may enter the female atrium at the dorsal side or the ventral side. The classification of this two features allows four combinations:

  1. Species with a penis papilla and with oviducts entering dorsally. These species continued in the genus Geoplana, because this is the combination that occurs in Geoplana vaginuloides.
  2. Species with a penis papilla and with oviducts entering ventrally. These species passed to the genus Gigantea.
  3. Species without a penis papilla and with oviducts entering dorsally. These species were named Notogynaphallia.
  4. Species without a penis panilla and with oviducts entering ventrally. This is the opposite of what is found in Geoplana. These species were transfered to a genus named Pasipha.


Things were starting to get more organized. Despite still having more than a hundred species, the genus Geoplana was a little more homogeneous now. But by the beginning of the 21th century, more detailed studies on the internal anatomy of planarians demonstrated that other parts of the body also had taxonomic importance. Furthermore, molecular studies were now available and the genus was challenged by the molecular phylogeny. The already expected result was confirmed. A study of molecular phylogeny by Fernando Carbayo and colleagues in 2013 revealed that the genus Geoplana, as defined by Ogren and Kawakatsu, was still a mess. Species were separated in several groups that needed to received their own genera. These new genera created from Geoplana were: Barreirana, Cratera, Matuxia, Obama and Paraba.



At the end the type species, Geoplana vaginuloides, remained almost alone. The only other species that grouped with it was Geoplana chita. The genus Geoplana, once with hundreds of species throughout the whole world, now has only two species restriced to the Atlantic Forest between the Brazilian states of Rio de Janeiro and Paraná. And guess which of the new genera received most of the species one in Geoplana?
















Yes, we can!

Yes, we can!

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Carbayo, F., Álvarez-Presas, M., Olivares, C., Marques, F., Froehlich, E., & Riutort, M. (2013). Molecular phylogeny of Geoplaninae (Platyhelminthes) challenges current classification: proposal of taxonomic actions Zoologica Scripta, 42 (5), 508-528 DOI: 10.1111/zsc.12019

Darwin, C. 1844. Brief description of several terrestrial planariae, and of some remarkable marine species, with an account of their habits. Annals and Magazine of Natural History, Annales de Sciences Naturelles, 14: 241-251.

Diesing. K. M. 1850. Systema helminthum. Academia Caesareae Scientiarium.

Fletcher, J. J.; Hamilton, A. G. 1887. Notes on Australian land-planarians, with descriptions of some new species. Part I. Proceedings of the Linnean Society of New South Wales, 2: 349-374.

Froehlich, E. M. 1955. Sôbre espécies brasileiras do gênero GeoplanaBoletim da Faculdade de Filosofia, Ciências e Letras da Universidade de São Paulo, Série Zoologia, 19: 289-339.

Gay, Claudio. 1849. Historia fisica y politica de Chile. Vol. 3.

Gmelin, O. F. 1788. Systema Naturae. Moseley, H. N. 1877. Notes on the structure of several forms of land planarians with a description of two new genera and several new species, and a list of all species at present known. Quarterly Journal of Microscopical Sciences, 17: 274-292.

Ogren, R.; Kawakatsu, M. 1990. Index to the species of the family Geoplanidae (Turbellaria, Tricladida, Terricola) Part I: Geoplaninae. Bulletin of Fuji Women’s College, 28: 79-166.

Schultze, M.; Müller, F. 1857. Beiträge zur Kenntnis der Landplanarien. Abhandlungen der Naturforschenden Gesellschaft zu Halle, 4: 61-74.

Stimpson, W. 1857. Prodromus descriptionis animalium evertebratorum quae in expeditione ad Oceanum, Pacificum Septentrionalem a Republica Federata missa Johanne Rodgers Duce, observavit et descripsit. Pars I. Turbellaria Dendrocoela. Proceedings of the Academy of Natural Sciences of Philadelphia, 19-31.

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Filed under Molecular Biology, Systematics, taxonomy, worms, Zoology

42: the answer to life, the universe and everything (i.e., consciousness)

by Piter Kehoma Boll

ResearchBlogging.orgIn his work  “The Hitchhiker’s Guide to the Galaxy”, Douglas Adams defined that the answer to life, the universe and everything is 42.

Now a group of scientists measured glucose metabolism in brains in a resting state from coma patients in order to determine the mean metabolic activity and used this value to predict whether a patient in a comatose state would eventually regain consciousness.


A brain image taken with positron emission tomography (PET) after injecting [18F]-fluorodeoxyglucose (FDG), a radioactive form of glucose. This is the same method used in the study to quantify metabolic activity. Photo by Jens Maus.

The results indicate that the brain needs a minimum of 42% of normal metabolic activity in one of the hemispheres (the less injured one) in order to garantee consciousness recovery. And what is life, the universe and everything if not a consequence of our consciousness?


Deep Thought. Image extracted from

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Stender, J., Mortensen, K., Thibaut, A., Darkner, S., Laureys, S., Gjedde, A., & Kupers, R. (2016). The Minimal Energetic Requirement of Sustained Awareness after Brain Injury Current Biology DOI: 10.1016/j.cub.2016.04.024


Filed under Molecular Biology, Neurosciences

Acoelomorpha: A Phylogenetic Headache

by Piter Kehoma Boll

Take a look at these guys:

The green worm Symsagittifera roscoffensis (Graff, 1891). Photograph by Vincent Maran. Extracted from
Green worms Symsagittifera roscoffensis (Graff, 1891). Photograph by Vincent Maran. Extracted from

It’s a member of the group Acoelomorpha, animals which are still a puzzle in phylogeny. That means no one knows for sure where in the animals’ evolutionary tree they are exactly.

But first, let’s take a look at what makes an acoelomorph.

Those little guys are small worms, usually measuring less than 1 mm in length and living in marine or brackish waters or as symbionts. There are two groups of acoelomorphs: Acoela and Nemertodermatida. Acoels are the simplest ones; they have a mouth, but lack a gut, so that the food ingested goes directly to the internal tissues. In Nemertodermatida, there is a blind gut, i.e., with only one opening, like in the primitive cnidarians or in flatworms. In fact, they were initially classified as flatworms, but several features later challenged their position inside this phylum. The main differences are:

  • Acoelomorphs have an epidermis (“skin”) with cilia whose roots are interconnected in a hexagonal pattern, while other flatworms have independent cilia.
  • Acoelomorphs lack protonephridia (primitive kidney-like organs) and all other groups of animals have at least one of those or more complex organs with similar function.
  • While flatworms and all other protostomes (arthropods, annelids, mollusks, nematodes…) have ventral nerve cords and deuterostomes (chordates, echinoderms…) have dorsal ones, in acoelomorphs there are several nerve cords distributed radially along the body length.
Distribution of nerve chords in Acoelomorpha, Protostomia and Deuterostomia. Picture by myself, Piter K. Boll.
Distribution of nerve chords in Acoelomorpha, Protostomia and Deuterostomia. Picture by myself, Piter K. Boll.

Analyzing such features, it seems obvious that Acoelomorpha is a basal group of bilateral animals and may be the reminiscent of a primitive group of animals later almost completely extinct by their most complex descendants, the true protostomes and deuterostomes. The original radially-distributed nerve cords were simplified in dorsal or ventral ones in higher groups but remained radial in Acoelomorpha.

Several phylogenetic studies indicate that Acoelomorpha is indeed a basal group of bilateral animals. They also lack several important Hox genes (responsible for determining body plan and organs’ distribution in animals) and it is quite unlikely that they would have lost most of them by secondary simplification.

Another group of simple animals, the Xenoturubellida, was sometimes proposed as a sister group for Acoelomorpha. Their proximity would be explained by several shared features, mainly the simple nervous system, the lack of a stomatogastric (mouth-gut) system, the structure of the epidermal cilia and the unusual fact that, in both groups, epidermal degenerated cells as resorbed in the gastrodermis.

A Xenoturbella worm. Photograph extracted from
A Xenoturbella worm. Photograph extracted from Hiroaki_Nakano_eng/

The group Xenoturbellida, however, has been placed in Deuterostomia in some molecular studies and recently Philippe et al. 2011 proposed that Acoelomorpha would also belong to the Deuterostomia! But how could such a thing be possible when they obviously have primitive and unique features, like the radially placed nerve cords? The group’s explanation is that Acoelomorpha, as well as Xenoturbellida, have a sequence of microRNA (miR-103/107/2013) which is exclusive to Deuterostomia, so they would also be deuterostomes.

But wait a minute! What do they mean by “exclusive to Deuterostomia”? It means that that microRNA sequence is found in deuterostomes, but not in protostomes. Now think with me. We have 4 bilateral groups here: Acoelomorpha, Xenoturbellida, Deuterostomiaa and Protostomia. If you look at them this way, we can see that the statement “miR-103/107/2013 is exclusive to Deuterostomia” is false. The truth is that this sequence is absent in Protostomia but present in all other groups. Wouldn’t it be more logical to think that, instead of deuterostomes acquiring this sequence, what really happened is that it was a primitive microRNA and protostomes have lost it?

If you consider Xenoturbellida and Acoelomorpha inside Deuterostomia, you have to assume that they passed through a huge simplification, and you maintain the radial nerve cords unexplained. Now if you think of them as primitive groups, the only thing necessary is to analyze protostomes as having lost a microRNA sequence. Quite a simpler explanation which doesn’t let open gaps.

Phylogenetic position of Acoelomorpha and Xenoturbellida according to Philippe et al. 2011. It means that (1) the bilaterians' ancestor had a complex set of Hox Genes; (2) miR-103/107/2013 appeared in an ancestor of true Deuterostomes+Xenacoelomorpha (Xenoturbellida + Acoelomorpha); (3) Xenacoelomorpha passed through a huge loss of Hox genes, loss of most internal organs and a mysterious set of radial nerve cords appear. Very complicated.
Phylogenetic position of Acoelomorpha and Xenoturbellida according to Philippe et al. 2011. It means that (1) the bilaterians’ ancestor had a complex set of Hox genes, being a complex animal; (2) miR-103/107/2013 appeared in an ancestor of true Deuterostomes+Xenacoelomorpha (Xenoturbellida + Acoelomorpha); (3) Xenacoelomorpha passed through a huge loss of Hox genes, loss of most internal organs and a mysterious set of radial nerve cords appear. Very complicated.
Position of Xenacoelomorpha as a basal group. It means that (1)
Phylogenetic position of Acoelomorpha and Xenoturbellida according to Boll et al. 2013 (that’s me!) based on a review of previous studies, as a basal group. It means that (1) the bilaterian’s ancestor was a simple animal, with a simple set of Hox genes, having miR-103/107/2013 and radial nerve cords; (2) the set of Hox genes became more complex and the nerve cords where simplified to either dorsal or ventral; (3) miR-103/107/2013 is lost in Protostomia. Way simpler.

You can read more in the references listed below.

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Boll, P., Rossi, I., Amaral, S., Oliveira, S., Müller, E., Lemos, V., & Leal-Zanchet, A. (2013). Platyhelminthes ou apenas semelhantes a Platyhelminthes? Relações filogenéticas dos principais grupos de turbelários. Neotropical Biology and Conservation, 8 (1), 41-52 DOI: 10.4013/nbc.2013.81.06

Egger, B., Steinke, D., Tarui, H., De Mulder, K., Arendt, D., Borgonie, G., Funayama, N., Gschwentner, R., Hartenstein, V., Hobmayer, B., Hooge, M., Hrouda, M., Ishida, S., Kobayashi, C., Kuales, G., Nishimura, O., Pfister, D., Rieger, R., Salvenmoser, W., Smith, J., Technau, U., Tyler, S., Agata, K., Salzburger, W., & Ladurner, P. (2009). To Be or Not to Be a Flatworm: The Acoel Controversy. PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005502

Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G., Edgecombe, G., Martinez, P., Baguna, J., Bailly, X., Jondelius, U., Wiens, M., Muller, W., Seaver, E., Wheeler, W., Martindale, M., Giribet, G., & Dunn, C. (2009). Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings of the Royal Society B: Biological Sciences, 276 (1677), 4261-4270 DOI: 10.1098/rspb.2009.0896

Moreno, E., Nadal, M., Baguñà, J., & Martínez, P. (2009). Tracking the origins of the bilaterian patterning system: insights from the acoel flatworm. Evolution & Development, 11 (5), 574-581 DOI: 10.1111/j.1525-142X.2009.00363.x

Mwinyi, A., Bailly, X., Bourlat, S., Jondelius, U., Littlewood, D., & Podsiadlowski, L. (2010). The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis. BMC Evolutionary Biology, 10 (1) DOI: 10.1186/1471-2148-10-309

Philippe, H., Brinkmann, H., Copley, R., Moroz, L., Nakano, H., Poustka, A., Wallberg, A., Peterson, K., & Telford, M. (2011). Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature, 470 (7333), 255-258 DOI: 10.1038/nature09676


Filed under Evolution, Molecular Biology, Zoology

Why thymine instead of uracil?

by Piter Kehoma Boll About a year ago, while I was in my class of Techniques of Molecular Diagnosis, an interesting doubt sprouted: why does DNA use thymine instead of uracil as RNA does?

I hope everybody reading this knows about nucleic acids and the difference between DNA and RNA. As a very quick review:

RNA (ribonucleic acid) is a polymer made of ribonucleotides, compound molecules made of three parts, or smaller molecules: a nitrogenous base (adenine, uracil, cytosine or guanine), a ribose sugar and a phosphate group.

DNA (deoxyribonucleic acid) is similar, but instead of uracil it has thymine, and instead of a ribose sugar is has a deoxyribose, so that it is made of deoxyribonucleotides. Another difference is that DNA is a double chain twisted helicoidally, where two nitrogenous bases (each from one of the chains) are connected. Adenine is always connected to thymine and cytosine always to guanine, so that one chain is always dependent on the other.

Currently it’s highly accepted that RNA was the first nucleic acid to exist and that DNA evolved from it, so the changes in the sugar and one of the nitrogenous bases must have some advantage.

To understand that, let’s take a look at the structure of the uracil:


The only difference between it and thymine is the presence of a methyl group thymine:


In fact, thymine is also called 5-methyluracil. But let’s go to the explanation:

While nucleotides are synthesized, the nucleotide-monophosphates (NMPs), i.e., the set nitrogenous base + sugar + phosphate is dehydroxylated, creating 2’-deoxy-nucleotide-monophosphate (dNMPs), i.e., GMP, AMP, CMP and UMP (for guanine, adenine, cytosine and uracil) are changed to dGMP, dAMP, dCMP and dUMP.

This modification by dehydroxylation has been shown to make the phosphodiester bonds (the bonds of phosphates on the sugar) less susceptible to hydrolysis and damage by UV radiation. It assures that a DNA molecule will not be as easy to be broken as an RNA molecule, which is very useful since DNA carries all the information to build up the organism.

After the dehydroxilation of the nucleotide-monophosphates, the next step, catalyzed by folic acid, add a methyl group to the uracil to form a thymine, so turning dUMP into dTMP.

There are many explanations for that:

1. Despite uracil’s tendency to pair with adenine, it can also pair with any other base, including itself. By adding a methyl group (which is hydrophobic) and turning it into thymine, its position is reorganized in the double-helix, not allowing those wrong pairings to happen.

2. Cytosine can deaminate to produce uracil. You can see in the picture below that the only difference between them is the change from an O in uracil to an NH2 in cytosine. The problem is that, if uracil were a component of DNA, the repair systems would not be able to distinguish original uracil from uracil originated by deamination of cytosine. So using thymine instead makes it way easier and more stable, as any uracil inside DNA must come from a cytosine and so it can be replaced by a new cytosine.


This didn’t evolve for that purpose, of course. Evolution cannot predict what happens. Probably during the earliest times of life, eventually an error changed uracil for thymine and it was found to be more stable to carry information, since such a molecule wouldn’t be destroyed so easily and thus would succeed in passing its “layout” to the next generation.

It makes me wonder… Could some alien life form have found an alternative way to deal with RNA’s (or something equivalent) instability?

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Main Reference:

Jonsson, J. (1996). The Evolutionary Transition from Uracil to Thymine Balances the Genetic Code Journal of Chemometrics, 10, 163-170 DOI: 10.1002/(SICI)1099-128X(199603)10:2


Filed under Evolution, Molecular Biology