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- Mikkelsen, Tarjei S, et al.
(författare)
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7141, s. 167-177
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Tidskriftsartikel (refereegranskat)abstract
- We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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- Lawniczak, Mara K. N., et al.
(författare)
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Standards recommendations for the Earth BioGenome Project
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (refereegranskat)abstract
- A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
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| 11. |
- Lewin, Harris A., et al.
(författare)
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The Earth BioGenome Project 2020 : Starting the clock
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 119:4
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 12. |
- Lillie, Mette, et al.
(författare)
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Variation in Major Histocompatibility Complex diversity in invasive cane toad populations
- 2017
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Ingår i: Wildlife research (East Melbourne). - 1035-3712 .- 1448-5494. ; 44:6-7, s. 565-572
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Tidskriftsartikel (refereegranskat)abstract
- Context. The cane toad (Rhinella marina), a native species of central and southern America, was introduced to Australia in 1935 as a biocontrol agent after a complex history of prior introductions. The population rapidly expanded and has since spread through much of the Australian landmass, with severe impacts on the endemic wildlife, primarily via toxicity to predators. The invasion process has taken its toll on the cane toad, with changes in the immunological capacity across the Australian invasive population.Aims. To investigate the immunogenetic underpinnings of these changes, we studied the diversity of the Major Histocompatiblity Complex (MHC) genes in introduced cane toad populations.Methods. We studied the diversity of two MHC genes (the classical class I UA locus and a class II DAB locus) and compared these with neutral microsatellite markers in toads from the Australian site of introduction and the Australian invasion front. We also included toads from Hawai'i, the original source of the Australian toads, to infer founder effect.Key results. Diversity across all markers was low across Australian and Hawai'ian samples, consistent with a reduction in genetic diversity through multiple founder effects during the course of the successive translocations. In Australia, allelic diversity at the microsatellite markers and the UA locus was reduced at the invasion front, whereas all three alleles at the DAB locus were maintained in the invasion-front toads.Conclusions. Loss of allelic diversity observed at the microsatellite markers and the UA locus could be the result of drift and bottlenecking along the invasion process, however, the persistence of DAB diversity warrants further investigation to disentangle the evolutionary forces influencing this locus.Implications. Through the use of different molecular markers, we provide a preliminary description of the adaptive genetic processes occurring in this invasive population. The extremely limited MHC diversity may represent low immunogenetic competence across the Australian population, which could be exploited for invasive species management.
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- Millar, Alexander J., et al.
(författare)
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Searching for dark matter with plasma haloscopes
- 2023
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Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 107:5
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Tidskriftsartikel (refereegranskat)abstract
- We summarize the recent progress of the Axion Longitudinal Plasma Haloscope (ALPHA) Consortium, a new experimental collaboration to build a plasma haloscope to search for axions and dark photons. The plasma haloscope is a novel method for the detection of the resonant conversion of light dark matter to photons. ALPHA will be sensitive to QCD axions over almost a decade of parameter space, potentially discovering dark matter and resolving the strong CP problem. Unlike traditional cavity haloscopes, which are generally limited in volume by the Compton wavelength of the dark matter, plasma haloscopes use a wire metamaterial to create a tuneable artificial plasma frequency, decoupling the wavelength of light from the Compton wavelength and allowing for much stronger signals. We develop the theoretical foundations of plasma haloscopes and discuss recent experimental progress. Finally, we outline a baseline design for ALPHA and show that a full-scale experiment could discover QCD axions over almost a decade of parameter space.
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- Zhao, Yaofeng, et al.
(författare)
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Ornithorhynchus anatinus (Platypus) Links the Evolution of Immunoglobulin Genes in Eutherian Mammals and Nonmammalian Tetrapods
- 2009
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Ingår i: Journal of Immunology. - : The American Association of Immunologists. - 0022-1767 .- 1550-6606. ; 183:5, s. 3285-3293
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Tidskriftsartikel (refereegranskat)abstract
- The evolutionary origins of mammalian immunoglobulin H chain isotypes (IgM, IgD, IgG, IgE, and IgA) are still incompletely understood as these isotypes differ considerably in structure and number from their counterparts in nonmammalian tetrapods. We report in this study that the platypus (Ornithorhynchus anatinus) Ig H chain constant region gene locus contains eight Ig encoding genes, which are arranged in an mu-delta-o-gamma 2-gamma 1-alpha 1-epsilon-alpha 2 order, spanning a total of similar to 200 kb DNA, encoding six distinct isotypes. The o (o for Ornithorhynchus) gene encodes a novel Ig H chain isotype that consists of four constant region domains and a hinge, and is structurally different from any of the five known mammalian Ig classes. This gene is phylogenetically related to nu (epsilon) and gamma, and thus appears to be a structural intermediate between these two genes. The platypus delta gene encodes ten heavy chain constant region domains, lacks a hinge region and is similar to IgD in amphibians and fish, but strikingly different from that in eutherian mammals. The platypus Ig H chain isotype repertoire thus shows a unique combination of genes that share similarity both to those of nonmammallian tetrapods and eutherian animals and demonstrates how phylogenetically informative species can be used to reconstruct the evolutionary history of functionally important genes.
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