Monday, November 22, 2010

Rethinking Genomic Structures

                                                  Oikopleura dioica (source)

In a fascinating find, investigators described the genomic sequence of a tiny, transparent, mucus-covered marine animal, as the "alien-genome". Reason? It simply shatters a lot of our etched-in-stone scientific notions about eukaryotic genome architecture.
The genome of Oikopleura dioica breaks all the organizational rules previously thought to be critical for animal genomes - turning on its head a long held scientific-belief, that common architectural features of genomes observed across all animal kingdoms, are maintained by natural selection. 
This  study goes on to show that genome arrangement could actually be rather plastic!
The belief: Decades of arduous scientific work has shown that there exists a remarkable similarity in genome organization between species as distant and diverse as humans and sea sponges. These common multiple genomic features includes the order of genes, intron-exon organization, transposon diversity and developmental gene repertoire. This enormous amount of data somehow (mis)-led many of us to infer that a designated, non-flexible animal genome architecture is necessary to preserve form and function and is actively maintained by natural selection.
As it turns out, the genome of this tunicate, Oikopleura shatters this long-held belief!
About the animal: Tunicates are viewed as the closest living relatives of vertebrates, were probably simplified from more complex chordate ancestors.
Larvacean tunicates represent the second most abundant component of marine zooplankton and filter small particles by their gelatinous house which it secretes from a terminally differentiated oikplastic epithelium. Oikopleura dioica is the most cosmopolitan larvacean, has a very short life cycle (4 days at 20°C) and can be reared in the laboratory for hundreds of generations. Unique among tunicates, it has separate sexes. In fact, Oikopleura dioica is a favorite model-system for genetic, genomic and embryological studies.
The effort: Over 50 collaborating researchers at the Sars International Centre for Marine Molecular Biology at the University of Bergen in Norway, together with colleagues at Genoscope, a national sequencing center in France, sequenced and analyzed the Oikopleura genome, with high coverage shotgun reads (14X) using males.
At only 70 million base pairs (Mb), it turned out to be the smallest known animal genome. Remarkably, with 18,020 predicted genes, almost as much as a human's, but tucked into a DNA sequence 40 times shorter, makes the Oikopleura genome unusually compact. Although, two exceptions to global compaction are particularly interesting, as they may illustrate where excessive reduction could be harmful. First, a small population of Oikopleura developmentally regulated transcription factor genes have relatively large introns and intergenic spaces, and second, genes on the Y chromosome (since sex is genetically defined in Oikopleura), all expressed in the testis during spermatogenesis, have giant introns.
Moreover, while animals from sea anemones to primates have conserved the physical location of certain genes near each other, Oikopleura's genes appeared to have been randomly located, almost shuffled. Yet, Oikopleura has many of the same essential phenotypic features as other tunicates with traditional genome architecture.
Another significant peculiarity was the locations of introns - another structural feature conserved across several phyla - was gone, yet newer introns (5 to 6) had emerged all over the genome, sharing sequence-similarity to neighbours. This perhaps adds another dimension to the old scientific debate - where do introns originate?
Additionally, the Oikopleura genome leacked genes involved in immunity. In fact, many conserved immunity genes failed detection, supporting a minimized immune system consistent with the short Oikopleura life history.
Reason: Experts suggest that Oikopleura, is a rapidly evolving animal, with constant mutations in its nuclear and mitochondrial genomes. This speedy evolution is likely due to the fact that the animal spends most its life just below the ocean surface, bombarded by UV rays and other mutagens. Evolution of this rate, might have resulted this distinctively different genomic-architecture, unparalled in the animal kingdom. 
Overall, this work suggests that multiple genome organization features, have dramatically changed in the Oikopleura lineage. And despite an unprecedented genome revolution, the Oikopleura lineage preserved essential morphological features, even maintaining the chordate body plan to the adult stage.
It also throws up interesting questions..
-How does Oikopleura deal with this immense radiation induced DNA-damage? Does it have a unique DNA-recombination-repair mechanism?
-Fundamentally, why do larger animals (like us) need larger genomes?

* Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate.
  Science, published online 18 November 2010, doi:10.1126/science.1194167.
* Thomson group, working on Oikopleura.

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