36
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes.

          Abstract

          Adaptive radiations are well-known for animals and plants, but not for microbes. Here, Hehemann et al. show that there has been a recent adaptive radiation of bacteria in the Vibrionaceae to use different forms of alginate and that this radiation has been mediated by horizontal gene transfer.

          Related collections

          Most cited references44

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              dbCAN: a web resource for automated carbohydrate-active enzyme annotation

              Carbohydrate-active enzymes (CAZymes) are very important to the biotech industry, particularly the emerging biofuel industry because CAZymes are responsible for the synthesis, degradation and modification of all the carbohydrates on Earth. We have developed a web resource, dbCAN (http://csbl.bmb.uga.edu/dbCAN/annotate.php), to provide a capability for automated CAZyme signature domain-based annotation for any given protein data set (e.g. proteins from a newly sequenced genome) submitted to our server. To accomplish this, we have explicitly defined a signature domain for every CAZyme family, derived based on the CDD (conserved domain database) search and literature curation. We have also constructed a hidden Markov model to represent the signature domain of each CAZyme family. These CAZyme family-specific HMMs are our key contribution and the foundation for the automated CAZyme annotation.
                Bookmark

                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                22 September 2016
                2016
                : 7
                : 12860
                Affiliations
                [1 ]Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, USA
                [2 ]Microbiology Graduate Program, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, USA
                [3 ]Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, USA
                [4 ]Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, USA
                [5 ]Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, USA
                [6 ]Broad Institute , Cambridge, Massachusetts 02139, USA
                Author notes
                [*]

                These authors contributed equally to this work

                [†]

                Present address: MARUM Center for Marine Environmental Sciences, University of Bremen Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany

                [‡]

                Present address: Department of Electrical Engineering and Computer Science/Institute Center Smart Infrastructure (iSmart), Masdar Institute, 54224 Abu Dhabi, United Arab Emirates

                [§]

                Present address: Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA

                [∥]

                Present address: AbVitro, Inc. 27 Drydock Ave, Boston, Massachusetts, USA

                Author information
                http://orcid.org/0000-0003-1237-2314
                Article
                ncomms12860
                10.1038/ncomms12860
                5036157
                27653556
                f33b6ae9-ecf6-4ff8-a260-da358126ae86
                Copyright © 2016, The Author(s)

                This work is licensed under a Creative Commons Attribution 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/4.0/

                History
                : 25 February 2016
                : 09 August 2016
                Categories
                Article

                Uncategorized
                Uncategorized

                Comments

                Comment on this article