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Platypus Genome Sequenced; Provides Clues to Mammalian Evolution

NEW YORK (GenomeWeb News) – An international team of scientists today reported that it has sequenced the genome of one of the most unusual creatures on earth: the platypus.
In a paper published online today in Nature, the team described this feat — along with some of its conclusions about the evolution of this furry, egg-laying, duck-billed, milk-producing, toothless, and venomous animal. Five additional papers, published in the journal Genome Research this week, apply information discovered from the platypus genome to specific research on everything from venom production to RNA pathways to development.
The platypus genome is expected to augment monotreme conservation efforts. And, researchers say, having the platypus genome on hand will also aid comparative mammalian studies.
With its apparent combination of mammalian, reptilian, avian, and unique features, the platypus has long puzzled biologists. Along with other egg-laying mammals such as echidna, the platypus belongs to a taxonomic group called Monotremata, often considered a sub-class of mammals that branched off an estimated 160 to 210 million years before so-called therians — marsupials (Marsupialia) and placental mammals (Placentalia). It has 52 chromosomes, ten of which are sex chromosomes.
Among its most notable features, the platypus has a sensitive electro-sensory system that it uses to capture invertebrate prey, and a unique venom system: males are venomous during mating season, with venom being released from spurs in the animals’ hind legs.
Lead author Wes Warren, assistant director of Washington University School of Medicine’s Genome Sequencing Center, and his colleagues used whole-genome shotgun methods to sequence the 2.2 billion base pairs in the platypus (Ornithorhynchus anatinus) genome to about six times coverage. This proved no small task, given that roughly half of the platypus genome is made up of repetitive sequence.
From the 1.84 gigabases of assembled sequence — obtained from 26 million reads — they ordered 437 megabases onto 20 chromosomes, localizing sequences by fluorescence in situ hybridization. Not surprisingly, the authors found, “[t]he platypus genome, as well as the animal, is an amalgam of ancestral reptilian and derived mammalian characteristics.”
Even so, there were some unexpected finds. For example, the platypus genome contains an unanticipated number of small nucleolar RNAs — about ten times as many as therian mammals. As for its other small RNA pathways, some are similar to mammals, while others are more similar to birds, specifically chickens. The researchers also found a group of some 183 new miRNAs that appear to be unique to platypus and echidna. The majority of these belonged to nine clusters, five of which are on the X1 chromosome.
Two of the accompanying papers in Genome Research describe these platypus RNA pathways in more detail. The first, by senior author Gregory Hannon, a Cold Spring Harbor Laboratory biologist, and his colleagues focuses on platypus small RNA. For that study, Hannon and his colleagues deep sequenced six platypus and echidna tissues to better understand small RNA pathways and their tissue-specific expression.
The second, by University of Münster experimental pathologist Jurgen Brosius and his colleagues, deals specifically with the more than 200 platypus snoRNAs. By comparing them with those in other mammalian and vertebrate groups, Brosius and his team found new features in platypus snoRNAs that provide insights into snoRNA evolution.
Based on the Ensembl pipeline, Warren and his team predicted that the platypus genome contains 18,527 protein-coding genes — approximately the same number as humans and opossum. They also did whole-genome alignments between the platypus sequence and sequence from human, dog, mouse, opossum, and chicken, and looked at the genetics behind characteristic platypus features.
“Of particular interest are families of genes involved in biology that links monotremes to reptiles, such as egg-laying, vision, and envenomation, as well as mammal-specific characters such as lactation, characters shared with marsupials such as antibacterial proteins, and platypus-specific characters such as venom delivery and underwater foraging,” the authors wrote. 
In a separate paper in Genome Research, senior author Katherine Belov, a veterinary researcher at the University of Sydney, and her colleagues looked more closely at the evolution of genes related to the platypus’ venom and venom delivery system and to their defensin genes in general.
Meanwhile, senior author Jennifer Marshall Graves, a biologist at the Australian National University, and her team published a Genome Research paper comparing platypus sex chromosomes with those of other animals. They concluded that platypus sex chromosomes are distinct from those of therians and are more similar to those of birds.
Finally, senior author Sheau Teddy Hsu, an obstetrics and gynecology researcher at Stanford University, led a group of researchers who used information about platypus genetics to help them understand testicular descent in therian mammals. That work is also appearing in Genome Research this week.
“The fascinating mix of features in the platypus genome provides many clues to the function and evolution of all mammals,” Richard Wilson, director of Washington University’s Genome Center and senior author of the Nature paper, said in a statement. “By comparing the platypus genome to other mammalian genomes, we’ll be able to study genes that have been conserved through evolution.”
The platypus genome sequence is available online at GenBank.

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