How was the genome of non-avian dinosaurs arranged?

A high-quality Emu genome helps to reconstruct the evolution of avian chromosomes.

Although the non-avian dinosaurs receive a lot of media attention – especially the iconic Tyrannosaurus rex – their genetic evolution is largely ignored by journalists. However, we can probe the fascinating genomic history of non-avian dinosaurs by studying their modern descendants, the birds (see for example this book chapter). Most bird species have about 10 large macrochromosomes, accompanied by 30 smaller microchromosomes. Over time, numerous chromosomal sections have been rearranged, both within and between chromosomes (as I recently described in sandpipers). Hence, if we want to reconstruct a genomic picture of the non-avian dinosaurs, we need to look at the bird species with the slowest chromosomal evolution. Generally, evolutionary biologists have assumed that ratites – a group of flightless birds, including the ostrich and kiwis – show the slowest rate of evolution on the avian phylogeny. But is that really the case?

Reptilian Rearrangements

In a recent study in the journal Genome Research, researchers produced a high-quality assembly of the Emu (Dromaius novaehollandiae) genome. To assess the rate of chromosomal evolution in this species, they compared its genome and several other avian genomes with a set of reptiles: the Green Sea Turtle (Chelonia mydas), the Prairie Rattlesnake (Crotalus viridis), and the American Alligator (Alligator mississippiensis). This comparison revealed that the Emu underwent fewer chromosomal rearrangements than the other bird species, suggesting that it is a good proxy for the ancestral condition in birds. In other words, the genome of non-avian dinosaurs probably looked like the Emu genome.

Chromosomal comparisons between the Emu and several reptiles (top figures) reveals that this species experienced fewer genomic rearrangements than other bird species (bottom figure). From: Liu et al. (2021).

Nuclear Puzzle

Now that we have established that the genome of non-avian dinosaurs is comparable with that of the Emu, we can move one step further. How are the chromosomes arranged in the nucleus? Studies in Chicken (Gallus gallus) showed that microchromosomes are huddled together in the center while macrochromosomes are located at the periphery (owls, by the way, are an interesting exception). This arrangement probably relates to the activity of the genes on these chromosomes. Microchromosomes have a higher gene density and are transcriptionally more active. Macrochromosomes are less active and tend to be tightly packed (i.e. as heterochromatin). That is the situation in Chicken, what about the Emu?

To solve this mystery, the researchers turned to Hi-C sequencing, which is a technique to identify contacts within (cis-contacts) and between (trans-contacts) different chromosomes. If the Emu genome is similarly organized in the nucleus, we would expect to see more trans-contacts between the active microchromosomes in the center than between the inactive macrochromosomes at the periphery. And that was indeed the case. Because the genome of the Emu is close to the ancestral condition in birds, the genomes of non-avian dinosaurs were probably arranged in a similar way.

A simplified overview of the organization of micro- and macrochromosomes in the nucleus of the Emu. Notice the higher number of trans-contacts between the microchromosomes. From: Liu et al. (2021).

Non-avian Dinosaur DNA

Can we now conclude that the genomes of all non-avian dinosaurs, from Ankylosaurus to Zapalasaurus, were arranged in this way? Not exactly, the findings of this Emu study only provided insights into the ancestral chromosomal condition of birds. To reconstruct the genome of the common ancestor of avian and non-avian dinosaurs we would have to go back further in time. Moreover, numerous other species split off from that distant ancestor and probably evolved their specific chromosomal differences. The genome of a Tyrannosaurus likely looked quite different from the genome of a Triceratops. Each species has a unique evolutionary trajectory with its own peculiarities. An important nuance to keep in mind (and that is often neglected by journalists). Nonetheless, it seems reasonable to assume that the genome of non-avian dinosaurs was packed into the nucleus with microchromosomes in the center and macrochromosomes at the periphery. There will undoubtedly have been some exceptions. Whether we can ever identify these outliers is another question.

References

Liu, J., Wang, Z., Li, J., Xu, L., Liu, J., Feng, S., … & Zhou, Q. (2021). A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Research, 31(3), 497-511.

Featured image: Emu (Dromaius novaehollandiae) © H. Zell | Wikimedia Commons

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