The fugu is a famous fish, at least as a Japanese sushi dish containing a potentially lethal neurotoxin that was featured on an episode of The Simpsons. Fugu is a member of the pufferfish group, which have another claim to fame: an extremely small genome, roughly a tenth the size of that of other vertebrates. The genome of several species of pufferfish is being sequenced, and the latest issue of Nature announces the completion of a draft sequence for the green spotted pufferfish, Tetraodon nigroviridis, a small freshwater species.
Tetraodon has about the same number of genes as we do, 20,000-25,000, but they are contained in a total genome length of 340Mb vs. our huge 3.1Gb. One major difference is that in Tetraodon, transposable elements are rare: they have 73 types, present in less than 4000 copies, but humans have about 20 different types present in millions of copies. Transposable elements may be reverse transcriptases that blindly copy RNA sequences back into the DNA (called LINES) or shorter sequences that are processed by LINES, called SINES. These really are parasitic bits of selfish DNA, and somehow, pufferfish seem to be largely free of them.
One of the interesting things one can do with a pair of genome sequences is to start mapping synteny. Synteny represents the preservation of small regions of order within a chromosome; while the overall organization may have been scrambled by millions of years of chromosome breaks and fusions and duplications and deletions, we can still identify smaller blocks that maintain the same series of genes within them. For example, if we look on a chromosome of one organism and we see the series of genes A-B-C-D-E-F, and we look in another organism and find a chromosome with the genes W-X-C-D-E-Y-Z, we can see that the C-D-E chunk can be mapped directly to one region of that second organism’s chromosome.
A way to diagram this is to color code all the syntenic regions from each chromosome in one organism, and see how those regions are distributed in a second organism. For instance, in the first diagram below, imagine that human chromosome 15 has been colored yellow (the key along the bottom of the diagram tells you how they’ve been color coded.) Then, we take each synteny with chromosome 15 in the Tetraodon genome and color it yellow; you can think of it as if we’ve taken human chromosome 15, and all the other chromosomes, and broken them apart and reassembled them into the Tetraodon genome, and the colors allow us to see where each fragment came from. For instance, you can see that large pieces of human chromosome 15 are found in Tetraodon chromosomes 5 and 13.
You can also do this in the other direction, and take each Tetraodon chromosome, color code them, break them apart, and reassemble them into the order they would be in in the human genome, as in the second diagram.
What you are seeing in the scattered colors in these diagrams is a rendering of the history of chromosome reorganization that occurred during evolution. Hundreds of millions of years of juggling, and the order is still not completely randomized—there are still recognizably preserved blocks of local structure.
Of course, don’t be misled by the synteny diagrams into thinking that what happened in evolution was the reorganization of the human genomic organization into the Tetraodon pattern (or vice versa). There was a common ancestor with some arrangement of genes on its chromosomes, and those chromosomes got broken apart and juggled around in our history, and those chromosomes were independently scrambled in the Tetraodon lineage.
Here’s something else we can learn from synteny. Looking more closely at the map, below, reveals a curious pattern: some of the Tetraodon chromosomes can be mapped in an alternating or interleaved arrangement on the human chromosomes.
For instance, look at human chromosome 16 (Hsa16). Blocks of genes from Tetraodon chromosome 5 (Tni5) and Tetraodon chromosome 13 (Tni13) are both found in a larger syntenic region here…and this defies probability. If chromosome reorganizations were random, we shouldn’t be seeing only Tni5 and Tni13 alternating exclusively here, and we shouldn’t be seeing these other associations all over the place. You can also see Tni5 and Tni13 alternating on Hsa15, and Tni1 and Tni7 alternating on HsaX.
Why are Tni5 and Tni13 found together, and Tni1 and Tni7, and Tni2 and Tni3, and so forth? The simplest answer is that there was a whole genome duplication in the Tetraodon lineage. In the last common ancestor of humans and Tetraodon, there was a single chromosome that mapped onto that region of Hsa16. After Tetraodon diverged, that chromosome was duplicated, forming Tni5 and Tni13, and over time, many of the duplicated genes were secondarily lost, but which copy was lost, whether the one on Tni5 or the one on Tni13, was random. The regions of doubly-conserved synteny (DCS), where we’ve got pairs of Tetraodon chromosomes clustering together in lockstep with regions of the human chromosome, represent ghosts of a single ancestral chromosome. In this diagram, those hypothetical ancestral chromosomes have been outlined and colored in the pastel colors surrounding the interleaved regions, and given the names AncA, AncB, AncC, etc. There are 110 of these DCS blocks scattered through the genome, and they can be grouped into 12 ancestral chromosomes.
And here you are, those ancestral syntenic fragments can then be reordered into a their simplest arrangement, and we have an ancestral genome.
I don’t know about you, but I find this use of genomic evidence and logic to identify the long-lost chromosomes of a 350 million-year-old organism to be extremely cool. Hella cool. Kick-ass, far-out, mega-cool.
Jebus, but I am so happy to be a member of the reality-based community.
Anyway, comparative genomics now lets us put together a comprehensible story of the evolution of vertebrates. In the diagram below, we start with an ancestral bony fish with 12 chromosomes, and then split into two lineages that lead to us tetrapods on the left, and modern fish on the right.
Our lineage was marked by a period of intense amplification of transposable elements, LINES and SINES and repeated junk that copied itself over and over, leading to our current grossly bloated genome, containing 20-25 thousand genes swimming in 3 Gb of mostly useless dead DNA. Meanwhile, the fish went through a whole genome duplication (WGD), followed by a thorough pruning back of many of the excess copies, leaving them with a similar 20-25 thousand genes. In the Tetraodon lineage, at least, there was no amplification of junk, so their protein-coding genes reside in a lean, trim 340 Mb.
Comparative genomics is a powerful tool that is going to be telling us much, much more about our evolutionary history.
…the remarkable preservation of the Tetraodon genome after WGD makes it possible to infer the history of vertebrate chromosome evolution. The model suggests that the ancestral vertebrate genome was comprised of 12 chromosomes, was compact, and contained not significantly fewer genes than modern vertebrates(in as much as the WGD and subsequent massive gene loss resulted in only a tiny fraction of duplicate genes being retained).
The explosion of transposable elements in the mammalian lineage,subsequent to divergence from the teleost lineage, may have provided the conditions for increased interchromosomal rearrangements in mammals; in contrast, the Tetraodon genome underwent much less interchromosomal rearrangement. With the availability of additional vertebrate genomes (dog, marsupial, chicken, medaka, zebrafish and frog are underway), it will be possible to explore intermediate nodes such as the last common ancestor of amniotes, of sarcopterygians and of actinopterygians, and to gain an increasingly clearer pictureof the early vertebrate ancestor. Because the early vertebrate genome is ‘closer’ to current invertebrates, this should in turn facilitate comparison between vertebrate and invertebrate evolution.
Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.