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      The others: our biased perspective of eukaryotic genomes

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          Abstract

          Understanding the origin and evolution of the eukaryotic cell and the full diversity of eukaryotes is relevant to many biological disciplines. However, our current understanding of eukaryotic genomes is extremely biased, leading to a skewed view of eukaryotic biology. We argue that a phylogeny-driven initiative to cover the full eukaryotic diversity is needed to overcome this bias. We encourage the community: (i) to sequence a representative of the neglected groups available at public culture collections, (ii) to increase our culturing efforts, and (iii) to embrace single cell genomics to access organisms refractory to propagation in culture. We hope that the community will welcome this proposal, explore the approaches suggested, and join efforts to sequence the full diversity of eukaryotes.

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          The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

          Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.
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            The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

            The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11 472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond.
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              CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

              A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial eukaryotes.
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                Author and article information

                Journal
                8805125
                20449
                Trends Ecol Evol
                Trends Ecol. Evol. (Amst.)
                Trends in ecology & evolution
                0169-5347
                1872-8383
                30 January 2015
                11 April 2014
                May 2014
                27 February 2015
                : 29
                : 5
                : 252-259
                Affiliations
                [1 ]Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
                [2 ]University of British Columbia, Vancouver, BC, Canada
                [3 ]Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
                [4 ]American Type Culture Collection, Manassas, VA, USA
                [5 ]Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
                [6 ]Departament de Genètica, Universitat de Barcelona, Barcelona, Catalonia, Spain
                [7 ]Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
                Author notes
                Corresponding authors: del Campo, J. ( javier.delcampo@ 123456botany.ubc.ca ); Ruiz-Trillo, I. ( inaki.ruiz@ 123456multicellgenome.org )
                Article
                EMS62053
                10.1016/j.tree.2014.03.006
                4342545
                24726347
                c17dd341-cde6-4d4d-aac1-a04b0ebf0fca
                © 2014 The Authors. Published by Elsevier Ltd.

                This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/3.0/).

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                Categories
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                Ecology
                eukaryotic genomics,phylogeny,ecology,eukaryotic tree of life,culture collections,culturing bias,single cell genomics

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