Platypus genome unravels mysteries of mammalian evolution

Genome Research is publishing several papers related to analyses of the duck-billed platypus (Ornithorhynchus anatinus) genome sequence. The place of (egg-laying) monotremes, such as the platypus, in mammalian evolutionary history has remained controversial. Now, researchers are finding that the distinctive anatomical and physiological properties of the platypus are reflected in the newly sequenced platypus genome. Through comparative genomics, the platypus genome is providing remarkable insights into the evolution of venom components, the sex-determination system, testicular descent, and small RNA pathways. Primary research reports describing these novel insights will appear online May 8, concurrent with publication of the platypus genome sequence report in the journal Nature. 1. Evolution of platypus venom peptides

Platypus is the only mammal delivering venom through a "spur" situated on the inside of each hind limb. While searching the platypus genome for the molecular signatures of cysteine-rich antimicrobial peptides, called defensins, in an investigation into the role of defensins in monotreme immunity, researchers uncovered genes coding for components of platypus venom. Further analysis revealed that these venom genes evolved by gene duplication of antimicrobial beta-defensins. Interestingly, this finding mirrors an independent evolutionary pathway in reptiles. "Snake venom crotamines have also evolved from beta-defensins in separate gene duplication events, making this a compelling example of convergent evolution," says study leader Dr. Katherine Belov of the University of Sydney.

Reference: Whittington, C.M., Papenfuss, A.T., Bansal, P., Torres, A.M., Wong, E.S.W., Deakin, J.E., Graves, T., Alsop, A., Schatzkamer, K., Kremitzki, C., Ponting, C.P., Temple-Smith, P., Warren, W.C., Kuchel, P.W., and Belov, K. Defensins and the convergent evolution of platypus and reptile venom genes. Genome Res. doi:10.1101/gr.7149808.

Contact: Katherine Belov, Ph.D., University of Sydney, Sydney, Australia. (k.belov@usyd.edu.au, +61-293513454) or Camilla Whittington, University of Sydney, Sydney, Australia (+61-421851793)

2. Platypus genome reveals small RNA evolution and novel biology

Small non-coding RNAs have garnered significant interest for their ability to regulate gene expression. Two papers published by Genome Research have utilized the platypus genome sequence to investigate the conservation of small RNAs and associated functional pathways in the mammalian lineage. In the first study, researchers led by Dr. Gregory Hannon of Cold Spring Harbor Laboratory took a deep-sequencing approach to analyze small RNAs isolated from tissues of platypus and the echidna, another monotreme mammal. The isolated sequences were then mapped and compared to known small RNAs to identify conserved and novel RNA species. “Remarkably, we found that the platypus shares microRNA families uniquely with other mammals, but also uniquely with a representative of birds and reptiles,” explains Hannon. “Thus, the unusual morphology of these animals is also reflected at the genomic level and at the level of its small RNAs.”

The second paper describes an investigation of small nucleolar RNAs (snoRNAs) that sheds light on the evolution of this class of mammalian non-protein-coding RNAs. In addition to characterizing more than 200 snoRNAs in the platypus genome, researchers led by Dr. Jürgen Schmitz of the University of Münster made a particularly intriguing finding: evolution of a novel, platypus-specific snoRNA dispersal process. “Small nucleolar RNAs are rather stationary and, thus, not found in high copy numbers within mammalian genomes,” describes Schmitz. “We discovered an exceptional chimera, however, of a housekeeping snoRNA and a more mobile retroposon-like, non-LTR transposable element (RTE)-related sequence, which facilitated the mobility of the novel ‘snoRTE’ and the distribution of more than 40,000 copies, several of them actively expressed.”

Reference: Murchison, E.P., Kheradpour, P., Sachidanandam, R., Smith, C., Hodges, E., Xuan, Z., Kellis, M., Grützner, F., Stark, A., and Hannon, G.J. Conservation of small RNA pathways in platypus. Genome Res. doi:10.1101/gr.73056.107.

Contact: Gregory J. Hannon, Ph.D., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. (hannon@cshl.edu, +1-516-367-8847)

Reference: Schmitz, J., Zemann, A., Churakov, G., Kuhl, H., Grützner, F., Reinhardt, R., and Brosius, J. Retroposed SNOfall – A mammalian-wide comparison of platypus snoRNAs. Genome Res. doi:10.1101/gr.7177908.

Contact: Jürgen Schmitz, Ph.D., Institute of Experimental Pathology, University of Münster, Münster, Germany. (jueschm@uni-muenster.de, +49-251-8352133)

3. Bird-like sex-determination system of mammalian ancestors

Therian mammals possess an XY sex-determination system, where females have a pair of X chromosomes, and males harbor one X and one Y chromosome. However, the sex-determination system of platypus stands in stark contrast: the female has five different pairs of X chromosomes, while males have five X chromosomes and five Y chromosomes. In a study carried out at the Australian National University in Canberra, scientists used physical mapping of chromosomes to investigate homology and the evolutionary relationships between platypus and therian sex chromosomes.

“Surprisingly, we find that the platypus sex chromosomes are unrelated to the X or Y chromosomes of other mammals, and lack the mammalian sex determining gene SRY and the gene from which it evolved,” explains co-first author Dr. Paul Waters. “Instead, their sex chromosomes share extensive homology to those of birds.” Waters notes that this finding suggests our ancient mammal-like reptile ancestor may have had bird-like sex chromosomes and sex determination system.

Reference: Veyrunes, F., Waters, P.D., Miethke, P., Rens, W., McMillan, D., Alsop, A.E., Grützner, F., Deakin, J.E., Whittington, C.M., Schatzkamer, K., Kremitzki, C.L., Graves, T., Ferguson-Smith, M.A., Warren, W., Graves, J.A.M. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res. doi:10.1101/gr.7101908.

Contact: Paul D. Waters, Ph.D., Australian National University, Canberra, Australia. (waters@rsbs.anu.edu.au, +61-2-61253612)

4. Tracing the evolution of mammalian testicular descent

Researchers have made significant progress in determining the genetic mechanisms underlying mammalian physiological characteristics, but tracing the evolution of these features has proven difficult due to limited availability of vertebrate genome sequences, particularly of organisms basal to mammalian evolution. Now, the platypus genome sequence allows scientists to investigate the evolutionary origins of therian mammal characteristics by comparative analysis with a monotreme mammal. In this paper, researchers from the Stanford University School of Medicine and Chang Gung Memorial Hospital in Taiwan investigated the evolution of testicular descent, a therian adaptation for optimal spermatogenesis. The group identified critical evolutionary steps associated with the molecular signaling pathway that mediates testicular descent: gene duplication, followed by functional diversification of each of the daughter genes.

“This study highlights the immense opportunity to investigate the evolution and the underpinning genetic events of many lineage-specific adaptations in humans and other vertebrates using comparative genome analyses together with molecular techniques,” remarks corresponding author Dr. Sheau Yu Teddy Hsu.

Reference: Park, J., Semyonov, J., Chang, C.L., Yi, W., Warren, W., and Hsu, S.Y.T. Origin of INSL3-mediated testicular descent in therian mammals. Genome Res. doi:10.1101/gr.7119108.

Contact: Sheau Yu Teddy Hsu, Ph.D., Stanford University School of Medicine, Stanford, CA. (teddyhsu@stanford.edu, +1-650-723-7057)

Please direct requests for pre-print copies of the manuscripts to Peggy Calicchia, Genome Research Editorial Secretary (calicchi@cshl.edu; +1-516-422-4012).

Source: Cold Spring Harbor Laboratory