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      Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

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          Abstract

          The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation, and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Though it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism, and responses to external stimuli may reflect adaptations for surviving in this harsh environment.

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          Most cited references54

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          The genome sequence of the malaria mosquito Anopheles gambiae.

          Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
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            Reorganizing the protein space at the Universal Protein Resource (UniProt)

            The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.
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              Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

              As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.
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                Author and article information

                Journal
                101528555
                37539
                Nat Commun
                Nat Commun
                Nature communications
                2041-1723
                5 August 2014
                12 August 2014
                2014
                12 February 2015
                : 5
                : 4611
                Affiliations
                [1 ]Department of Genetics, Stanford University, 300 Pasteur Dr., Stanford, CA 94305, USA
                [2 ]School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA
                [3 ]Department of Entomology, Ohio State University, 300 Aronoff Laboratory, 318 W. 12th Ave., Columbus, OH 43210, USA
                [4 ]Department of Evolution, Ecology and Organismal Biology, Ohio State University, 300 Aronoff Laboratory, 318 W. 12th Ave., Columbus, OH 43210, USA
                [5 ]Department of Biology, Stanford University, 371 Serra St., Stanford, CA 94305, USA
                [6 ]Institut des Sciences de l'Evolution, UMR5554 CNRS-Université Montpellier 2, Montpellier Cedex 05, France
                [7 ]Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
                [8 ]Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
                [9 ]Department of Entomology, Texas A&M University, College Station, TX 77843, USA
                [10 ]Department of Zoology, Miami University, Oxford, OH 45056, USA
                Author notes
                Correspondence and requests for materials should be addressed to JLK joanna.l.kelley@ 123456wsu.edu or DLD denlinger.1@ 123456osu.edu
                [*]

                these authors contributed equally

                Article
                NIHMS612183
                10.1038/ncomms5611
                4164542
                25118180
                124fd136-cd66-4083-bbbf-0beb5fb14f1c
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