Unlocking Sea Anemone Secrets: Diving Deep into Repeatome Diversity

Hey there! Let’s talk about something super cool that makes up a huge chunk of the genetic code in pretty much every living thing, including those gorgeous, wavy creatures living on the seafloor: sea anemones! I’m talking about repetitive DNA, often called the “repeatome.” Think of it like the background music or maybe even the wild, unpredictable parts of a genome – it’s everywhere, and it does… well, a lot of things we’re still figuring out.

For ages, we looked at genomes with older tools, like checking chromosome shapes or measuring DNA size. These gave us a basic map. But now, with whole genome sequencing, we can read the *actual* letters of the genetic code. This is like going from a blurry satellite image to a street-level view! And when we zoom in, we see that a massive part of this genetic landscape is made of repeats. Seriously, in humans, it’s almost half the genome, and in something like maize, it can be up to a whopping 85%!

These repeats aren’t just random noise. They come in different flavors, like Transposable Elements (TEs) – the “jumping genes” that can copy and paste or cut and paste themselves around the genome – and satellite DNA (satDNA), which are short sequences repeated over and over, often found in specific spots like the ends or middle of chromosomes. TEs are like little genetic parasites sometimes, just making more copies of themselves, but they can also be surprisingly helpful, contributing to how organisms adapt or handle stress. On the flip side, they can cause trouble, messing up genes or rearranging chromosomes. SatDNA also evolves super fast, often changing a lot even between closely related species.

Studying these repeats is crucial because they evolve so quickly and are so dynamic. They can tell us a lot about how genomes change over time and contribute to the amazing diversity we see in life. But because they’re so shifty, building good databases of repeats is a real headache! Existing databases like Repbase and Dfam are great, but they don’t have a lot of data for many groups, and that includes our squishy friends, the sea anemones.

Why Sea Anemones? Why Now?

Sea anemones, and their cousins like corals and jellyfish (all part of a group called Cnidaria), are really important in the story of animal evolution. They branched off very early on the animal family tree, so studying their genomes gives us clues about the ancient history of all animals. Even though we’re getting more and more sea anemone genomes sequenced, most studies haven’t really dug deep into their repeat content. It’s like having a map of a city but ignoring all the bustling markets and hidden alleyways – you’re missing a huge part of the picture!

This lack of detailed repeat information for cnidarians in general, and sea anemones (Actiniaria) specifically, means it’s tough to really understand their genome diversity and how they evolved. Only a couple of sea anemone species were even represented in the main repeat databases. That felt like a challenge we had to tackle!

Building Our Special Toolkit: Actiniaria-REPlib

So, we decided to roll up our sleeves and build a really high-quality repeat database specifically for sea anemones. We called it Actiniaria-REPlib. Our goal was to create a tool that could find and classify repeats in sea anemone genomes much better than the general databases out there.

We gathered 37 publicly available sea anemone genomes and even assembled a new one ourselves from scratch – a lovely species called Actinostella flosculifera. Getting a good genome assembly is the first step, and it involves a lot of careful work, like cleaning up the raw DNA data, estimating the genome size, and piecing together millions of short DNA reads into longer sequences (like solving a giant puzzle!). We even assembled the mitochondrial genomes for many species, which are like tiny powerhouses with their own small genetic code, and used them to figure out how the species are related. This family tree helps us understand how repeat patterns might have changed as different sea anemone lineages evolved.

Once we had the genomes, the real work on repeats began. We used several sophisticated computer programs to find and identify repetitive sequences in each genome. Then, we combined all these findings into one big, initial library. But genomes are messy, and these programs can find slightly different versions of the same repeat or even find the same repeat multiple times. So, we had to clean it up, removing redundant sequences to create a refined library.

One of the biggest challenges was dealing with sequences the programs couldn’t immediately identify. These “unknown” repeats are like genetic mysteries! We threw more advanced tools at them, using different approaches like looking for specific protein signatures or using machine learning to try and classify them. It was a bit like getting different opinions from experts and then trying to figure out the truth when they sometimes disagreed. We developed a strategy to resolve these conflicts and assign the best possible classification.

After all this work, our Actiniaria-REPlib (version 1, because science is always moving forward!) ended up with a fantastic collection of 79,903 repeat sequences. We managed to classify most of them, identifying different types of TEs and tandem repeats.

Putting the Library to Work: What We Found

With our shiny new Actiniaria-REPlib in hand, we put it to the test. We used it to annotate the repetitive DNA in the 38 sea anemone genomes and compared the results to what we’d get using the older, more general databases like Repbase and the libraries generated by standard tools (RM2 lib). The difference was astounding!

Using Actiniaria-REPlib, we identified *way* more repetitive elements in every single genome. On average, our library found about 48.2% of the genome was repetitive DNA. Compare that to the average of only 8.4% found by RM2 lib or 7.8% found by Repbase. That’s roughly a 5 to 10 times increase in the amount of repetitive DNA we could even *see*! It really shows how much “dark matter” was hidden in these genomes when using less specific tools.

Within this newly revealed repeatome, we found that DNA transposons were generally the most common type, making up about 28.8% of the genomes on average, followed by LTR retrotransposons at around 10.1%. We also looked at genomes using lower-coverage sequencing data (like a quick snapshot instead of a full read) and found our library still did a great job of estimating the total repeat content and the proportions of different repeat classes.

Our mitochondrial DNA family tree mostly matched what other scientists have found, which is reassuring. It helps confirm that the species relationships we’re using to understand repeat evolution are solid.

Beyond Just Numbers: Stories in the Repeats

Having such a detailed view of the repeatome allowed us to see some really interesting patterns across different sea anemone species. It’s not just about the total amount of repeats; it’s also about *which* types are present and how they’re distributed.

For example, one species, Anthopleura sola, had a remarkably high amount of a specific type of TE called RC/Helitron compared to most other species we looked at. This species recently diverged from another closely related one, Anthopleura elegantissima. Comparing their repeatomes more closely in the future could tell us if this “burst” of Helitrons happened around the time they became separate species or if it’s something older they share.

We also noticed that some species known for being invasive, like Exaiptasia diaphana and Diadumene lineata, had relatively smaller genomes and smaller repeatomes. This is intriguing – could there be a link between repeat content and invasiveness?

On the other hand, some species with larger genomes, like Actinernus sp. and Actinoscyphia sp., also had a higher proportion of repetitive DNA overall. And certain groups had higher amounts of specific repeats, like LTRs or ribosomal RNA (rRNA) genes. These differences suggest that the repeatome isn’t just passively accumulating; it’s being shaped by evolutionary forces and might be playing a role in the unique biology of these different species.

Looking at “repeat landscapes” – graphs that show how much different repeats have diverged (changed) over time – we could see evidence of “repeat bursts.” This is when a specific type of repeat suddenly makes lots of copies of itself in the genome. We saw recent bursts of DNA transposons and LTRs across many species, and that notable, species-specific burst of RC/Helitrons in A. sola really stood out. These bursts are like genetic earthquakes, potentially reshaping the genome landscape.

Why This Matters and What’s Next

This study is, as far as we know, the first time anyone has done such a detailed, large-scale annotation of repetitive DNA for an entire group of cnidarians like sea anemones. It really highlights how much we were missing by relying on general databases. Our Actiniaria-REPlib library and the methods we used are a big step forward. They allow us to see much more of the genome’s repetitive content and compare it across species with much higher resolution.

This detailed view opens up exciting new questions. How do different sea anemone lineages end up with different sets of repeats? Could these repeats be repurposed over evolutionary time for new jobs, maybe influencing how genes are controlled or even contributing to the amazing diversity of forms and functions we see in sea anemones?

The work also points to some challenges for the wider scientific community. Annotating repeats is hard, and there’s no single perfect way to do it. Also, when scientists publish new genomes, they often don’t share the detailed repeat information they found, even if they calculated it. This makes it hard for others to check their work or use that data for new studies. We really need better standards for how repeat data is shared and deposited in public databases.

For Actiniaria-REPlib itself, this is just the beginning. As more sea anemone genomes are sequenced (especially from species we haven’t included yet) and as repeat annotation tools get even better, we can update and improve the library. Manual curation – having experts carefully check and refine the repeat classifications – will also make it even more accurate.

Ultimately, we hope our work provides a solid foundation and inspires similar efforts for other groups within Cnidaria and beyond. Understanding the repeatome isn’t just about counting repeats; it’s about unlocking a major part of the genome that plays a vital, though often mysterious, role in evolution and diversity. And for sea anemones, these hidden genetic landscapes are finally starting to come into view!

Source: Springer