When studying such complex topics as wholesale body replication and regeneration of limbs, it is a heady subject to tackle all at once. And it’s unlikely that beginning on something the size of mammals, using model organisms or not, is going to reveal anything at all without a basic understanding of how regeneration is supposed to work. So scientists began at a smaller level, a much simpler one that was already known to have this capability.
Enter the planarians, a group of loosely correlated flatworms that contain the mechanism for regenerating and duplicating themselves bow to stern if injured. This rapidity in regrowing themselves even works with only a single adult stem cell from the organism, implying that each of their collection of stem cells are programmed to rebirth the creature if separated from the rest of the body. These specialized cells, which it should be noted are only a small group in the body of a planarian, it isn’t all of their cells that can do this, are termed neoblasts and they are the only cells in the flatworms that actually divide.
Thanks to all of this, planarians, specifically the species Schmidtea mediterranea, are used as a model organism in stem cell research and in fields investigating the process of regeneration. But to be a good model organism, preferably everything has to be known about the species and, at minimum, the genome should be sequenced so that traits can be matched to the genetic code. And the planarian of interest’s genome is not that large, only sitting around 1-2 Gigabases. Yet, until now, we’ve never had a proper fully sequenced genome for the species. Why is that?
Revealing The Cloaked Genome
One sticking point is the heavy amount of A-T bases in the genome, making up around 70% of the presented coding information. But the much larger reason wasn’t fully understood until recently, when German researchers from the Max Planck Institute and the Heidelberg Institute teamed up to finally decipher S. mediterranea’s genome. What they found was surprising in a number of ways.
To get the process to finally work, they borrowed the long-read MARVEL machine from the company Pacific Biosciences, which is able to sequence genomes in chunks that can be as long as 40,000 base pairs, as compared to the 100 to 500 base pairs that a normal sequencer can manage. It also excels at reading sequences that are low in complexity and this genome seems to be exactly that with its high repetitious content.
After checking over the obtained sequences and correlating the different 40k chunks to build the full genome, along with looking for and correcting any mistakes the machine might have made, they were finally ready to analyse what this finally unearthed model organism had to offer. The first thing they noticed is that the repetition of sequences in the genome exceeded 60%, far higher than the 40% average found in mammals.
Secret Repetition and Losses
Next, they identified an even more precise reason for the prior inability to sequence the species. The S. mediterranea genome features a huge amount of retroviral inserted long terminal repeats, 7,000 of them in fact. These are characterized by having hundreds or even thousands of repeated sequences in them and several of those found in this genome were more than 30 kilobases in length. That’s more than triple the size of what’s found in vertebrate genomes.
All of this showcases why shorter read sequencing machines were unable to successfully break down the genome arrangement. The lengthy repeat sections were confusing their placement in the overall sequence.
The following investigation looked into the differences between this exhibit planarian genome and all other organisms, trying to see what makes planarians unique. This task heavily focused on the highly conserved genes as good measures of differences. What was surprising here is that while the 452 lost genes in these regions matches up well with the losses of other invertebrate model organisms that have been studied, 124 of those genes were ones that were known to be essential in mammals and that are key components in multicellular life. This includes genes involved in repairing double strand breaks in DNA. How planarians are able to survive without these is still a mystery for now, but may give insight into why they are so resistant to certain types of DNA damaging radiation.
The Lack of Essential Functionality
Important metabolic genes working with fatty acid synthase were also lost, along with those used in heme breakdown. The former result is of special interest because the same loss was observed in the parasitic cousins of the flatworms, but it had been proposed then that losing those genes was a specific adaptation that helped with parasitism. Finding this same deletion in non-parasitic flatworms implies that the loss was something that happened to a common ancestral species, meaning it has nothing to do with parasitism in the first place.
Lastly, the biggest gene losses were of those named MAD1 and MAD2 that are used to prevent mismatching of chromosomes when producing daughter cells. In short, they arrest the cycle of mitotic division if the chromosomes aren’t split evenly between the two cells. As can be guessed, these genes are incredibly important in preventing cellular degeneration from mismatched chromosomes. While homologues to these genes have been identified in all the other non-planarian flatworms that have been studied, they were nowhere within S. mediterranea.
Despite this lack, tests have shown that planarians retain the ability to properly divide their chromosomes evenly, even without these genes or any identifiable genes matching them. What was found is that less studied gene complexes appear to help regulate this system even without MAD genes or it may be that MAD1 and MAD2 are still in the genome, but have lost all the identifying sequence markers that enable matching them to the known sequences. Either option is possible.
Onwards To Regeneration
Regardless, the loss of all these essential genes gives real question to the core cell components needed for a complex eukaryotic life form. And it may provide a greater understanding of just how the planarians are able to regenerate so readily and completely.
For now, further analysis of the model organism’s genome will be done to elucidate the genes that connect to their regeneration ability. With those in hand, real experimentation of the trait can be done, greatly opening up our scientific understanding of regeneration and what possibilities we have in using it to regrow limbs and other such feats of science fiction.
Photo CCs: Smed from Wikimedia Commons