We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

Marsupials differ from most other mammals in their method of reproduction, in that they have chosen, in an evolutionary sense, to develop lactation rather than placentation for the nurture of their young. The neonate is therefore born with a mixture of advanced and embryonic characters, and yet is readily accessible within the pouch, providing a unique system for the study of the ontogeny of various physiological and endocrinological parameters. Marsupials are therefore ideal animals for research into mammalian reproductive physiology. The results of this exciting new research are summarized in this book by two of the foremost workers in the field. Individual chapters analyse the genetic and hormonal control of sexual differentiation, male and female reproductive structures and their functions, the role of the corpus luteum in the oestrous cycle and pregnancy, the hormonal control of embryonic diapause and the role of the marsupial placenta in the development of the embryo. This book is more than just a straightforward review of marsupial reproduction for its detailed analyses and broad comparative coverage will attract mammalogists and reproductive physiologists with a wide range of research interests.

Background: Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. Many hypotheses have been advanced to explain why genomic imprinting evolved in mammals, but few have examined how it arose. The host defence hypothesis suggests that imprinting evolved from existing mechanisms within the cell that act to silence foreign DNA elements that insert into the genome. However, the changes to the mammalian genome that accompanied the evolution of imprinting have been hard to define due to the absence of large scale genomic resources between all extant classes. The recent release of the platypus genome has provided the first opportunity to perform comparisons between prototherian (monotreme; which appear to lack imprinting) and therian (marsupial and eutherian; which have imprinting) mammals. Results: We compared the distribution of repeat elements known to attract epigenetic silencing across the entire genome from monotremes and therian mammals, particularly focusing on the orthologous imprinted regions. There is a significant accumulation of certain repeat elements within imprinted regions of therian mammals compared to the platypus. Conclusions: Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long terminal repeats and DNA elements, in therian imprinted genes and gene clusters is coincident with, and may have been a potential driving force in, the development of mammalian genomic imprinting. These data provide strong support for the host defence hypothesis.

▪ Abstract Embryonic diapause, or delayed implantation as it is sometimes known, is said to occur when the conceptus enters a state of suspended animation at the blastocyst stage of development. Blastocysts may either cease cell division so that their size and cell numbers remain constant, or undergo a period of very slow growth with minimal cell division and expansion. Diapause has independently evolved on many occasions. There are almost 100 mammals in seven different mammalian orders that undergo diapause. In some groups, such as rodents, kangaroos, and mustelids, it is widespread, whereas others such as the Artiodactyla have only a single representative (the roe deer). In each family the characteristics of diapause differ, and the specific controls vary widely from lactational to seasonal, from estrogen to progesterone, or from photoperiod to nutritional. Prolactin is a key hormone controlling the endocrine milieu of diapause in many species, but paradoxically it may act either to stimulate or inhibit growth and activity of the corpus luteum. Whatever the speciesspecific mechanisms, the ecological result of diapause is one of synchronization: It effectively lengthens the active gestation period, which allows mating to occur and young to be born at times of the year optimal for that species.

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as ‘vulnerable’ due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala’s ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala’s survival in the wild.

Background: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.