Platypus Genomic DNA Sequence Revealed

    By Kevin E. Noonan --

Ever since it was discovered by European explorers at the end of the 18th Century, the duckbill platypus (Ornithorhynchus anatinus) has been a biological anomaly.  Fur-bearing and lactating like a mammal (although lactation is through the abdominal wall because the animal lacks nipples), the platypus reproduces by egg-laying like a chicken and produces a venom like a reptile.  The platypus is so strange that George Shaw, who named the animal, thought it was a hoax:  he is reported to have said "[i]t was impossible not to entertain some distant doubts as to the genuine nature of the animal."  On Thursday, Nature reported the complete nucleotide sequencing of the platypus genome by an international team headed by scientists from Washington University/St. Louis (see "Top billing for platypus at the end of evolution tree").  Not surprisingly, the platypus' phenotypic peculiarities are reflected in its DNA, but the sequence promises to reveal a great deal more than that about the evolution of chickens, reptiles, and mammals, including man.

The sequencing experiments were performed using genomic DNA from one animal, obtained from the Glenrock Station at new South Wales, Australia (and nicknamed "Glennie").  It was known prior to sequencing that the platypus karyotype has 52 chromosomes, which is reported in Nature to comprise 2.3 billions basepairs of genomic DNA.  These chromosomes are morphologically characterized as comprising a few large chromosomes and several smaller ones, "reminiscent," according to the Nature report, "of reptilian macro- and microchromosomes."  Included in the chromosomal complement are multiple sex chromosomes, including five "X" and five "Y" chromosomes, which have been observed to properly segregate in sperm and egg cells.  In addition, these chromosomes have a certain level of homology to the "Z" sex chromosomes found in birds.

The sequencing efforts identified repetitive elements as well as putative protein-coding sequences.  The study of repetitive elements is informative in at least two ways.  First, the pattern and number of such elements provides a historical record of genetic events (such as retrovirus-mediated retrotransposition) that can be used to relate evolutionary events between different species of different phylogenies.  Second, at least some of these repetitive elements comprise structural or regulatory molecules (such as miRNA) that can be informative about genome structure as well as phylogenetic relationships.

Overall, the authors found fewer of the predicted non-protein coding RNA species than expected from mammalian species (1220 RNA species in the platypus compared with 4421 species in human and 655 in chicken).  On the other hand, the platypus shows amplification of small nucleolar RNA (snoRNA)-encoding sequences (2000 species in platypus compared with 200 in mammals); snoRNA is used in RNA modifications, particularly ribosomal RNA.  Notably missing in platypus genomic DNA are L1-retrotransposons, a feature in common with chickens, and notably present is a novel short interspersed (SINE) element present at about 40,000 copies.  The complexity of these SINE elements suggests a rapid and relatively recent genomic proliferation from an ancestral element.  Interspersed repetitive elements of all types comprise almost one-half of the platypus genome, the most abundant of which are a 5-kb long-interspersed-element (LINE2; about 1.9 million copies) and a "non-autonomous SINE-companion" interspersed repeat (about 2.75 million copies) that has been extinct in the other branches of the amniote phylogenetic line about 60-100 million years ago.  Finally, the mean microsatellite coverage in the platypus genome were estimated to be 2.67 +/- 0.34%, which is significantly lower than all mammalian genomes sequenced to date and most resembles what has been observed in chicken genomic DNA.

Protein-coding DNA was analyzed globally for comparison with mammalian DNA, and specifically to identify genes related to the aspects of platypus phenotype characteristic for features identified with its putative mammalian, avian, and reptilian roots.  Globally, the platypus genome encodes 18,527 protein-coding genes, which is similar to both humans and opossum.  The majority of these genes (15,312 out of 18,596, or 82%) have orthologous sequences in five other species for which comparisons were made (human, mouse, dog, opossum, and chicken).  Instances of simple 1:1 correspondence between platypus genes and orthologous genes in other species were enriched for so-called housekeeping genes, such as those involved in cellular metabolism, gene expression (especially mRNA splicing), and DNA replication.  However, although there was no correlation found in the position of such orthologous genes on the smaller platypus chromosomes and chicken microchromosomes, there was "considerable sequence alignment similarity" between the platypus "X" chromosomes and the chicken Z sex chromosome.  In contrast, there were no orthologous gene alignments observed when platypus sex chromosomes were compared to human X chromosomes.  The authors opine that this implied platypus X chromosomes evolved "directly from a bird-like ancestral reptilian system."

Turning to specific genes, the authors report results obtained for reproduction and lactation, chemosensory abilities, venom-producing genes, and cellular immunity.  The platypus genome contains four proteins homologous to human zona pellucida proteins, in addition to two genes (ZPAX) homologous to genes in birds, fish, and amphibians.  The platypus contains a single vitellogenin gene (chickens have three vitellogenin genes, while mammals have none), but lack testes-specific protease genes found in mammals.  Platypus milk is similar to mammalian milk, comprising sugars, lipids, and milk proteins with nutritional, anti-microbial, and bioactive functions.  Platypus casein genes, encoding the most abundant milk proteins (as in mammalian milk) are located in a syntenic position (adjacent to tooth enamel matrix protein genes) in platypus and mammalian chromosomes.

The platypus chemoreception system was found to be encoded by large numbers of genes encoding odorant receptors V1R and V2R, although the majority of these genes were genetically-inactivated pseudogenes.  The numbers of these genes were lower than those found in mammals (specific comparisons were made with rat and mouse); the odorant receptor gene complement was found to be about one-half that found in mammals.  However, the number of platypus V1R genes encoding an undisrupted open reading frame was about 50% higher than in mouse, and is the largest number of such genes yet detected in animal genomic DNA.  The genetic expansion of these specific receptors may, the Nature authors speculate, be the result of adaptations for pheromonal communication or detecting water-soluble odorants; this possibility is consistent with the animal's reliance on "smell" when underwater (since their other senses are muted in that environment).

Platypus venom is a complex mixture of at least 19 different peptides, including defensin-like peptides (vDLPs), C-type natriuretic peptide (vCNP) and nerve growth factor (vNGF).  Sequencing revealed that the genes encoding these various peptides appeared to have been produced from duplications of genes having different (i.e., non-venomous) functions.  The authors' analysis supported the conclusion that venom production comprising defensin, C-type natriuretic peptide, and nerve growth factor genes occurred independently in platypus and reptiles.

Finally, the platypus genome was remarkable for encoding at least 214 natural killer receptor genes, compared with human (15 genes), rat (45 genes), or opossum (9 genes) genomic DNA.  The platypus genome shares the feature of gene expansions in the cathelicidin antimicrobial peptide gene family with opossum genomic DNA.

The authors conclude that the homologies and differences between platypus genomic DNA and the sequences of the mammalian and other species observed by their comparisons support the hypothesis that the platypus lineage (the Monotrema) diverged from the rest of the eutherian lineage about 166 million years ago, and that the genetic distance of echidna (Tachyglossus aculeatus) from platypus . . . predicts that the platypus last shared a common ancestor with the other member of the Monotrema, the echidna, about 21 million years ago.

The authors express the hope that continued explication of the results of studies on platypus genomic DNA will contribute to a better understanding of the evolutionary relationship between mammals, including man, and other animals.  What is clear is that the relationships of the genes and other genetic elements found in platypus genomic DNA are consistent with descent with modification from a common ancestor guided by natural selection, and frankly inconsistent with "intelligent design" precepts.

Comments

[Sean]

"What is clear is that the relationships of the genes and other genetic elements found in platypus genomic DNA are...inconsistent with "intelligent design" precepts."

While I respect your work on this site, that comment (whether from you or from the authors of the article, it's hard to tell where it originates) is entirely out of place.

Regardless of any merits in the evolution/ID debate, the experiment described in the article was certainly NOT designed to test the hypothesis of whether (or not) it is possible that higher beings are the work of an intelligent designer. Therefore, the stated conclusion is entirely out of place.

The statement appears to be included either as a form of pandering or with the intention of polarizing, but in any event, it is not reflective of any adherence to the scientific method.

[Kevin E. Noonan]

Sorry, Sean, but I think it's entirely appropriate. Not on the question of whether there is a Supreme Being; science cannot address, much less answer that question, and if that is how you took the comment then 1) my apologies and 2) I would agree with your assessment.

But the point is that for those who propose to answer the ultimate question using the intelligent design argument (which is just a 20th Century update on the 19th Century's Paley's Watch hypothesis), then my position is that the platypus is a perfect illustration of the problem with their argument. The existence of a creature like the platypus, to me, is the antithesis of the arguments about the perfection of living things and how nature demands an intelligent designer. While religion might, nature does not, and until the intelligent design folks can at least accommodate the platypus into their argument, I think it valid to point that out.

Thanks for the comment.

[Glen Kelley]

Kevin,
Perhaps this is the final proof of "intelligent design by committee"?

[Sean]

Kevin, thanks for the follow-up.

In the spirit of discourse, I would say that the statement you initially made would require its own lengthy elaboration on why it follows from the facts presented before it. In that context, it might be appropriate.

I simply think that, standing on its own, it is not appropriate in the context in which it was given. I mean, your follow-up comment only scratches the surface of the issues/arguments, and doesn't provide enough information to assess whether the statement is or is not supported by the facts.

As lawyers, we are comfortable taking a set of facts, making arguments from those facts, and drawing conclusions from the arguments and facts coupled together. I simply felt that your statement took the shortcut from facts to conclusions without providing the necessary level of argument, and was therefore out of place.

Best regards,

[Kevin E. Noonan]

Glen:

Isn't that traditionally the definition of a camel?

Thanks for the comment.

what is this called in Japanese?