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Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge

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      Abstract

      Anhydrobiosis represents an extreme example of tolerance adaptation to water loss, where an organism can survive in an ametabolic state until water returns. Here we report the first comparative analysis examining the genomic background of extreme desiccation tolerance, which is exclusively found in larvae of the only anhydrobiotic insect, Polypedilum vanderplanki. We compare the genomes of P. vanderplanki and a congeneric desiccation-sensitive midge P. nubifer. We determine that the genome of the anhydrobiotic species specifically contains clusters of multi-copy genes with products that act as molecular shields. In addition, the genome possesses several groups of genes with high similarity to known protective proteins. However, these genes are located in distinct paralogous clusters in the genome apart from the classical orthologues of the corresponding genes shared by both chironomids and other insects. The transcripts of these clustered paralogues contribute to a large majority of the mRNA pool in the desiccating larvae and most likely define successful anhydrobiosis. Comparison of expression patterns of orthologues between two chironomid species provides evidence for the existence of desiccation-specific gene expression systems in P. vanderplanki.

      Abstract

      The African chironomid midge, Polypedilum vanderplanki, is able to withstand extreme desiccation. Here the authors sequence the genomes of a desiccation-tolerant and desiccation-sensitive species of chironomid midge and pinpoint genes that may have a role in conferring resistance to desiccation.

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      Most cited references 65

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      A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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        MUSCLE: multiple sequence alignment with high accuracy and high throughput.

         Robert Edgar (2004)
        We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            Author and article information

            Affiliations
            [1 ]National Institute of Agrobiological Sciences (NIAS) , Tsukuba 305-8602, Japan
            [2 ]Institute of Fundamental Biology and Medicine, Kazan Federal University , Kazan 420008, Russia
            [3 ]ISS Science Project Office, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA) , Tsukuba 305-8505, Japan
            [4 ]Okinawa Institute of Science and Technology Graduate University (OIST) , Onna, Okinawa 904-0495, Japan
            [5 ]Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Moscow 119991, Russia
            [6 ]A. N. Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119991, Russia
            [7 ]Institute for Information Transmission Problems of the Russian Academy of Sciences , Moscow 127994, Russia
            [8 ]Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan , Ann Arbor, Michigan 48109, USA
            [9 ]Department of Genetics, Faculty of Biology, Lomonosov Moscow State University , Moscow 119991, Russia
            [10 ]Scientific Research Institute of Physico-Chemical Medicine, Federal Bio-Medical Agency of Russia , Moscow 119828, Russia
            [11 ]Department of Biological Sciences, Vanderbilt University , Nashville, Tennessee 37235, USA
            [12 ]Advanced Science Research Center, Kanazawa University , Kanazawa 920-0934, Japan
            [13 ]National Institute for Basic Biology (NIBB) , Okazaki 444-8585, Japan
            [14 ]Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies , Okazaki 444-8585, Japan
            [15 ]Institute of Cytology and Genetics of the Russian Academy of Sciences , Novosibirsk 630090, Russia
            Author notes
            [*]

            These authors contributed equally to this work

            Journal
            Nat Commun
            Nat Commun
            Nature Communications
            Nature Pub. Group
            2041-1723
            12 September 2014
            : 5
            25216354 4175575 ncomms5784 10.1038/ncomms5784
            Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

            This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/

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