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      The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations

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          Abstract

          The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Old, new and emerging functions of caspases.

            Caspases are proteases with a well-defined role in apoptosis. However, increasing evidence indicates multiple functions of caspases outside apoptosis. Caspase-1 and caspase-11 have roles in inflammation and mediating inflammatory cell death by pyroptosis. Similarly, caspase-8 has dual role in cell death, mediating both receptor-mediated apoptosis and in its absence, necroptosis. Caspase-8 also functions in maintenance and homeostasis of the adult T-cell population. Caspase-3 has important roles in tissue differentiation, regeneration and neural development in ways that are distinct and do not involve any apoptotic activity. Several other caspases have demonstrated anti-tumor roles. Notable among them are caspase-2, -8 and -14. However, increased caspase-2 and -8 expression in certain types of tumor has also been linked to promoting tumorigenesis. Increased levels of caspase-3 in tumor cells causes apoptosis and secretion of paracrine factors that promotes compensatory proliferation in surrounding normal tissues, tumor cell repopulation and presents a barrier for effective therapeutic strategies. Besides this caspase-2 has emerged as a unique caspase with potential roles in maintaining genomic stability, metabolism, autophagy and aging. The present review focuses on some of these less studied and emerging functions of mammalian caspases.
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              Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

              Current sequencing methods produce large amounts of data, but genome assemblies constructed from these data are often fragmented and incomplete. Incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. This means that methods attempting to estimate rates of gene duplication and loss often will be misled by such errors and that rates of gene family evolution will be consistently overestimated. Here, we present a method that takes these errors into account, allowing one to accurately infer rates of gene gain and loss among genomes even with low assembly and annotation quality. The method is implemented in the newest version of the software package CAFE, along with several other novel features. We demonstrate the accuracy of the method with extensive simulations and reanalyze several previously published data sets. Our results show that errors in genome annotation do lead to higher inferred rates of gene gain and loss but that CAFE 3 sufficiently accounts for these errors to provide accurate estimates of important evolutionary parameters.
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                Author and article information

                Contributors
                Role: Associate Editor
                Journal
                Genome Biol Evol
                Genome Biol Evol
                gbe
                Genome Biology and Evolution
                Oxford University Press
                1759-6653
                January 2020
                03 December 2019
                03 December 2019
                : 12
                : 1
                : 3534-3549
                Affiliations
                [1 ] Department of Genetic Medicine and Development , Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
                [2 ] Department of Entomology , University of Illinois at Urbana-Champaign
                [3 ] Department of Ecology and Evolution , Swiss Institute of Bioinformatics, University of Lausanne, Switzerland
                [4 ] Center for Molecular Biodiversity Research , Zoological Research Museum Alexander Koenig, Bonn, Germany
                [5 ] Department of Evolutionary Biology and Ecology , Albert Ludwig University, Institute of Biology I (Zoology), Freiburg, Germany
                [6 ] 3rd Zoological Department , Natural History Museum Vienna, Vienna, Austria
                Author notes
                Author information
                http://orcid.org/0000-0002-4146-6523
                http://orcid.org/0000-0001-8093-0950
                Article
                evz260
                10.1093/gbe/evz260
                6938034
                31778187
                1bbafaa4-3606-4df1-984f-6573b793d1cb
                © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 26 November 2019
                Page count
                Pages: 16
                Funding
                Funded by: Swiss National Science Foundation 10.13039/501100001711
                Award ID: 31003A_143936
                Funded by: Swiss National Science Foundation 10.13039/501100001711
                Award ID: PP00P3_1706642
                Categories
                Research Article

                Genetics
                two-pronged bristletails,entognatha,chemosensory genes,ionotropic receptors,gustatory receptors,photoreceptors

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