Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development: 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 2x 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.

The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the brachyury gene regulatory network

The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the brachyury gene regulatory network:

Abstract

Mid-tailbud Ciona intestinalis embryo expressing GFP driven by the notochord specific cis-regulatory module associated with the transcription factor Brachyury (green notochord cells). Embryos are counterstained with phalloidin (red) and DAPI (blue) to highlight F-actin and nuclei, respectively. From José-Edwards et al., Developmental Dynamics 240:1793–1805, 2011.

[Report] Three Periods of Regulatory Innovation During Vertebrate Evolution

[Report] Three Periods of Regulatory Innovation During Vertebrate Evolution: Patterns of vertebrate gene regulation have changed during the course of evolution.

Authors: Craig B. Lowe, Manolis Kellis, Adam Siepel, Brian J. Raney, Michele Clamp, Sofie R. Salama, David M. Kingsley, Kerstin Lindblad-Toh, David Haussler

Systems-biology approaches for predicting genomic evolution

Systems-biology approaches for predicting genomic evolution:

Systems-biology approaches for predicting genomic evolution

Nature Reviews Genetics 12, 591 (2011).
doi:10.1038/nrg3033

Authors: Balázs Papp, Richard A. Notebaart & Csaba Pál

Is evolution predictable at the molecular level? The ambitious goal to answer this question requires an understanding of the mutational effects that govern the complex relationship between genotype and phenotype. In practice, it involves integrating systems-biology modelling, microbial laboratory evolution experiments and large-scale mutational analyses

Fossil jawless fish from China foreshadows early jawed vertebrate anatomy

Fossil jawless fish from China foreshadows early jawed vertebrate anatomy:

Fossil jawless fish from China foreshadows early jawed vertebrate anatomy

Nature 476, 7360 (2011). doi:10.1038/nature10276

Authors: Zhikun Gai, Philip C. J. Donoghue, Min Zhu, Philippe Janvier & Marco Stampanoni

Most living vertebrates are jawed vertebrates (gnathostomes), and the living jawless vertebrates (cyclostomes), hagfishes and lampreys, provide scarce information about the profound reorganization of the vertebrate skull during the evolutionary origin of jaws. The extinct bony jawless vertebrates, or ‘ostracoderms’, are regarded as precursors of jawed vertebrates and provide insight into this formative episode in vertebrate evolution. Here, using synchrotron radiation X-ray tomography, we describe the cranial anatomy of galeaspids, a 435–370-million-year-old ‘ostracoderm’ group from China and Vietnam. The paired nasal sacs of galeaspids are located anterolaterally in the braincase, and the hypophyseal duct opens anteriorly towards the oral cavity. These three structures (the paired nasal sacs and the hypophyseal duct) were thus already independent of each other, like in gnathostomes and unlike in cyclostomes and osteostracans (another ‘ostracoderm’ group), and therefore have the condition that current developmental models regard as prerequisites for the development of jaws. This indicates that the reorganization of vertebrate cranial anatomy was not driven deterministically by the evolutionary origin of jaws but occurred stepwise, ultimately allowing the rostral growth of ectomesenchyme that now characterizes gnathostome head development.

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo [Developmental Biology]

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo [Developmental Biology]: "Segmentation of the Drosophila embryo begins with the establishment of spatially restricted gap gene-expression patterns in response to broad gradients of maternal transcription factors, such as Bicoid. Numerous studies have documented the fidelity of these expression patterns, even when embryos are subjected to genetic or environmental stress, but the underlying mechanisms for this transcriptional precision are uncertain. Here we present evidence that every gap gene contains multiple enhancers with overlapping activities to produce authentic patterns of gene expression. For example, a recently identified hunchback (hb) enhancer (located 5-kb upstream of the classic enhancer) ensures repression at the anterior pole. The combination of intronic and 5′ knirps (kni) enhancers produces a faithful expression pattern, even though the intronic enhancer alone directs an abnormally broad expression pattern. We present different models for “enhancer synergy,” whereby two enhancers with overlapping activities produce authentic patterns of gene expression."

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism: "Ty C. Voss, R. Louis Schiltz, Myong-Hee Sung, Paul M. Yen, John A. Stamatoyannopoulos, Simon C. Biddie, Thomas A. Johnson, Tina B. Miranda, Sam John, Gordon L. Hager. The glucocorticoid receptor (GR), like other eukaryotic transcription factors, regulates gene expression by interacting with chromatinized DNA response elements. Photobleaching experiments in livi...."