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      Genomes of Stigonematalean Cyanobacteria (Subsection V) and the Evolution of Oxygenic Photosynthesis from Prokaryotes to Plastids

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          Abstract

          Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.

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          Most cited references123

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          Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

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          The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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            MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

            K Katoh (2002)
            A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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              New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

              PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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                Author and article information

                Journal
                Genome Biol Evol
                Genome Biol Evol
                gbe
                gbe
                Genome Biology and Evolution
                Oxford University Press
                1759-6653
                2013
                7 December 2012
                January 2013
                7 December 2012
                : 5
                : 1
                : 31-44
                Affiliations
                1Institute of Genomic Microbiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
                2Institute of Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
                3IASMA Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige (TN), Italy
                4Institut Pasteur, Unité des Cyanobactéries, Paris, France
                5Institut Pasteur, Laboratoire Collection des Cyanobactéries, Paris, France
                6Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
                7School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
                8Research Department of Genetics Evolution and Environment, University College London, London, United Kingdom
                9Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
                10Present address: Aix-Marseille University, Laboratoire de Chimie Bactérienne (LCB), Marseille, France
                Author notes

                Data deposition: Genomes have been deposited in NCBI under accessions PRJNA104961, PRJNA104963, PRJNA104969, PRJNA104967, PRJNA104965, and PRJNA157363.

                Associate editor: John Archibald

                †These authors contributed equally to this work.

                Article
                evs117
                10.1093/gbe/evs117
                3595030
                23221676
                12ef82a4-0dc7-4032-84d9-c9126f678468
                © The Author(s) 2012. 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 Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 4 December 2012
                Page count
                Pages: 14
                Categories
                Research Article

                Genetics
                plastid evolution,endosymbiosis,phylogenomics,true-branching cyanobacteria,nitrogen fixation

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