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      Spider genomes provide insight into composition and evolution of venom and silk

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          Abstract

          Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk.

          Abstract

          Spiders use self-produced venom and silk for their daily survival. Here, the authors report the assembled genome of the social velvet spider and a draft assembly of the tarantula genome and, together with proteomic data, provide insights into the evolution of genes that affect venom and silk production.

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          Most cited references44

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          The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

          The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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            An algorithm for progressive multiple alignment of sequences with insertions.

            Dynamic programming algorithms guarantee to find the optimal alignment between two sequences. For more than a few sequences, exact algorithms become computationally impractical, and progressive algorithms iterating pairwise alignments are widely used. These heuristic methods have a serious drawback because pairwise algorithms do not differentiate insertions from deletions and end up penalizing single insertion events multiple times. Such an unrealistically high penalty for insertions typically results in overmatching of sequences and an underestimation of the number of insertion events. We describe a modification of the traditional alignment algorithm that can distinguish insertion from deletion and avoid repeated penalization of insertions and illustrate this method with a pair hidden Markov model that uses an evolutionary scoring function. In comparison with a traditional progressive alignment method, our algorithm infers a greater number of insertion events and creates gaps that are phylogenetically consistent but spatially less concentrated. Our results suggest that some insertion/deletion "hot spots" may actually be artifacts of traditional alignment algorithms.
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              Extreme diversity, conservation, and convergence of spider silk fibroin sequences.

              Spiders (Araneae) spin high-performance silks from liquid fibroin proteins. Fibroin sequences from basal spider lineages reveal mosaics of amino acid motifs that differ radically from previously described spider silk sequences. The silk fibers of Araneae are constructed from many protein designs. Yet, the repetitive sequences of fibroins from orb-weaving spiders have been maintained, presumably by stabilizing selection, over 125 million years of evolutionary history. The retention of these conserved motifs since the Mesozoic and their convergent evolution in other structural superproteins imply that these sequences are central to understanding the exceptional mechanical properties of orb weaver silks.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                06 May 2014
                : 5
                : 3765
                Affiliations
                [1 ]Department of Molecular Biology and Genetics, Aarhus University , 8000 Aarhus C, Denmark
                [2 ]Interdisciplinary Nanoscience Center (iNANO), Aarhus University , 8000 Aarhus C, Denmark
                [3 ]Department of Bioscience, Aarhus University , 8000 Aarhus C, Denmark
                [4 ]BGI-Tech, BGI-Shenzhen , Shenzhen 518083, China
                [5 ]Department of Biology, University of Copenhagen , 2100 Copenhagen, Denmark
                [6 ]Bioinformatics Research Center (BiRC), Aarhus University , 8000 Aarhus C, Denmark
                [7 ]CLC bio, Silkeborgvej 2 , 8000 Aarhus C, Denmark
                [8 ]Department of Clinical Medicine, Aarhus University , 8000 Aarhus C, Denmark
                [9 ]King Abdulaziz University , Jeddah 21441, Saudi Arabia
                [10 ]These authors contributed equally to this work
                Author notes
                Article
                ncomms4765
                10.1038/ncomms4765
                4273655
                24801114
                a2ff102f-9601-442c-b189-5d2d35e60501
                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 3.0 Unported 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/3.0/

                History
                : 07 August 2013
                : 31 March 2014
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