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  • 1
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    The amphioxus genome and the evolution of the chordate karyotype (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-06-20
    Description: Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Putnam, Nicholas H -- Butts, Thomas -- Ferrier, David E K -- Furlong, Rebecca F -- Hellsten, Uffe -- Kawashima, Takeshi -- Robinson-Rechavi, Marc -- Shoguchi, Eiichi -- Terry, Astrid -- Yu, Jr-Kai -- Benito-Gutierrez, E Lia -- Dubchak, Inna -- Garcia-Fernandez, Jordi -- Gibson-Brown, Jeremy J -- Grigoriev, Igor V -- Horton, Amy C -- de Jong, Pieter J -- Jurka, Jerzy -- Kapitonov, Vladimir V -- Kohara, Yuji -- Kuroki, Yoko -- Lindquist, Erika -- Lucas, Susan -- Osoegawa, Kazutoyo -- Pennacchio, Len A -- Salamov, Asaf A -- Satou, Yutaka -- Sauka-Spengler, Tatjana -- Schmutz, Jeremy -- Shin-I, Tadasu -- Toyoda, Atsushi -- Bronner-Fraser, Marianne -- Fujiyama, Asao -- Holland, Linda Z -- Holland, Peter W H -- Satoh, Nori -- Rokhsar, Daniel S -- BBS/B/12067/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/12067/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Jun 19;453(7198):1064-71. doi: 10.1038/nature06967.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563158" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chordata/classification/*genetics ; Conserved Sequence ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Duplication ; Genes/genetics ; Genetic Linkage ; Genome/*genetics ; Humans ; Introns/genetics ; Karyotyping ; Multigene Family ; Phylogeny ; Polymorphism, Genetic/genetics ; Proteins/genetics ; Synteny ; Time Factors ; Vertebrates/classification/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    The Trichoplax genome and the nature of placozoans (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-23
    Description: As arguably the simplest free-living animals, placozoans may represent a primitive metazoan form, yet their biology is poorly understood. Here we report the sequencing and analysis of the approximately 98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole-genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome shows conserved gene content, gene structure and synteny in relation to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signalling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Srivastava, Mansi -- Begovic, Emina -- Chapman, Jarrod -- Putnam, Nicholas H -- Hellsten, Uffe -- Kawashima, Takeshi -- Kuo, Alan -- Mitros, Therese -- Salamov, Asaf -- Carpenter, Meredith L -- Signorovitch, Ana Y -- Moreno, Maria A -- Kamm, Kai -- Grimwood, Jane -- Schmutz, Jeremy -- Shapiro, Harris -- Grigoriev, Igor V -- Buss, Leo W -- Schierwater, Bernd -- Dellaporta, Stephen L -- Rokhsar, Daniel S -- England -- Nature. 2008 Aug 21;454(7207):955-60. doi: 10.1038/nature07191.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Integrative Genomics and Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA. msrivast@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18719581" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Adhesion ; Conserved Sequence ; Extracellular Matrix/genetics ; Gene Expression Regulation, Developmental ; Genome/*genetics ; Germ Cells ; Humans ; Invertebrates/anatomy & histology/classification/*genetics/*physiology ; Phylogeny ; Reproduction/genetics ; Sequence Analysis, DNA ; Sex ; Signal Transduction ; Synteny ; Transcription Factors/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-07
    Description: Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Martin, F -- Aerts, A -- Ahren, D -- Brun, A -- Danchin, E G J -- Duchaussoy, F -- Gibon, J -- Kohler, A -- Lindquist, E -- Pereda, V -- Salamov, A -- Shapiro, H J -- Wuyts, J -- Blaudez, D -- Buee, M -- Brokstein, P -- Canback, B -- Cohen, D -- Courty, P E -- Coutinho, P M -- Delaruelle, C -- Detter, J C -- Deveau, A -- DiFazio, S -- Duplessis, S -- Fraissinet-Tachet, L -- Lucic, E -- Frey-Klett, P -- Fourrey, C -- Feussner, I -- Gay, G -- Grimwood, J -- Hoegger, P J -- Jain, P -- Kilaru, S -- Labbe, J -- Lin, Y C -- Legue, V -- Le Tacon, F -- Marmeisse, R -- Melayah, D -- Montanini, B -- Muratet, M -- Nehls, U -- Niculita-Hirzel, H -- Oudot-Le Secq, M P -- Peter, M -- Quesneville, H -- Rajashekar, B -- Reich, M -- Rouhier, N -- Schmutz, J -- Yin, T -- Chalot, M -- Henrissat, B -- Kues, U -- Lucas, S -- Van de Peer, Y -- Podila, G K -- Polle, A -- Pukkila, P J -- Richardson, P M -- Rouze, P -- Sanders, I R -- Stajich, J E -- Tunlid, A -- Tuskan, G -- Grigoriev, I V -- England -- Nature. 2008 Mar 6;452(7183):88-92. doi: 10.1038/nature06556.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UMR 1136, INRA-Nancy Universite, Interactions Arbres/Microorganismes, INRA-Nancy, 54280 Champenoux, France. fmartin@nancy.inra.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18322534" target="_blank"〉PubMed〈/a〉
    Keywords: Abies/microbiology/physiology ; Basidiomycota/enzymology/*genetics/*physiology ; Fungal Proteins/classification/genetics/metabolism ; Gene Expression Regulation ; Genes, Fungal/genetics ; Genome, Fungal/*genetics ; Hyphae/genetics/metabolism ; Mycorrhizae/enzymology/*genetics/*physiology ; Plant Roots/*microbiology/physiology ; Symbiosis/genetics/*physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-02-15
    Description: Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562698/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562698/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Nicole -- Westbrook, M Jody -- Young, Susan L -- Kuo, Alan -- Abedin, Monika -- Chapman, Jarrod -- Fairclough, Stephen -- Hellsten, Uffe -- Isogai, Yoh -- Letunic, Ivica -- Marr, Michael -- Pincus, David -- Putnam, Nicholas -- Rokas, Antonis -- Wright, Kevin J -- Zuzow, Richard -- Dirks, William -- Good, Matthew -- Goodstein, David -- Lemons, Derek -- Li, Wanqing -- Lyons, Jessica B -- Morris, Andrea -- Nichols, Scott -- Richter, Daniel J -- Salamov, Asaf -- Sequencing, J G I -- Bork, Peer -- Lim, Wendell A -- Manning, Gerard -- Miller, W Todd -- McGinnis, William -- Shapiro, Harris -- Tjian, Robert -- Grigoriev, Igor V -- Rokhsar, Daniel -- R01 CA058530/CA/NCI NIH HHS/ -- R01 CA058530-14/CA/NCI NIH HHS/ -- R01 GM077197/GM/NIGMS NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-01/HG/NHGRI NIH HHS/ -- R37 HD028315/HD/NICHD NIH HHS/ -- England -- Nature. 2008 Feb 14;451(7180):783-8. doi: 10.1038/nature06617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and the Center for Integrative Genomics, University of California, Berkeley, California 94720, USA. nking@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18273011" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Adhesion ; Conserved Sequence ; Eukaryotic Cells/classification/cytology/*metabolism ; Evolution, Molecular ; Extracellular Matrix/metabolism ; Gene Expression Regulation ; Genetic Speciation ; Genome/*genetics ; Hedgehog Proteins/chemistry/genetics ; Humans ; Introns/genetics ; Phosphotyrosine/metabolism ; *Phylogeny ; Protein Structure, Tertiary/genetics ; Receptors, Notch/chemistry/genetics ; Signal Transduction/genetics ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    The Phaeodactylum genome reveals the evolutionary history of diatom genomes (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-10-17
    Description: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bowler, Chris -- Allen, Andrew E -- Badger, Jonathan H -- Grimwood, Jane -- Jabbari, Kamel -- Kuo, Alan -- Maheswari, Uma -- Martens, Cindy -- Maumus, Florian -- Otillar, Robert P -- Rayko, Edda -- Salamov, Asaf -- Vandepoele, Klaas -- Beszteri, Bank -- Gruber, Ansgar -- Heijde, Marc -- Katinka, Michael -- Mock, Thomas -- Valentin, Klaus -- Verret, Frederic -- Berges, John A -- Brownlee, Colin -- Cadoret, Jean-Paul -- Chiovitti, Anthony -- Choi, Chang Jae -- Coesel, Sacha -- De Martino, Alessandra -- Detter, J Chris -- Durkin, Colleen -- Falciatore, Angela -- Fournet, Jerome -- Haruta, Miyoshi -- Huysman, Marie J J -- Jenkins, Bethany D -- Jiroutova, Katerina -- Jorgensen, Richard E -- Joubert, Yolaine -- Kaplan, Aaron -- Kroger, Nils -- Kroth, Peter G -- La Roche, Julie -- Lindquist, Erica -- Lommer, Markus -- Martin-Jezequel, Veronique -- Lopez, Pascal J -- Lucas, Susan -- Mangogna, Manuela -- McGinnis, Karen -- Medlin, Linda K -- Montsant, Anton -- Oudot-Le Secq, Marie-Pierre -- Napoli, Carolyn -- Obornik, Miroslav -- Parker, Micaela Schnitzler -- Petit, Jean-Louis -- Porcel, Betina M -- Poulsen, Nicole -- Robison, Matthew -- Rychlewski, Leszek -- Rynearson, Tatiana A -- Schmutz, Jeremy -- Shapiro, Harris -- Siaut, Magali -- Stanley, Michele -- Sussman, Michael R -- Taylor, Alison R -- Vardi, Assaf -- von Dassow, Peter -- Vyverman, Wim -- Willis, Anusuya -- Wyrwicz, Lucjan S -- Rokhsar, Daniel S -- Weissenbach, Jean -- Armbrust, E Virginia -- Green, Beverley R -- Van de Peer, Yves -- Grigoriev, Igor V -- England -- Nature. 2008 Nov 13;456(7219):239-44. doi: 10.1038/nature07410. Epub 2008 Oct 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CNRS UMR8186, Department of Biology, Ecole Normale Superieure, 46 rue d'Ulm, 75005 Paris, France. cbowler@biologie.ens.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923393" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Algal/analysis ; Diatoms/*genetics ; *Evolution, Molecular ; Genes, Bacterial/genetics ; Genome/*genetics ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    The Sorghum bicolor genome and the diversification of grasses (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-02-04
    Description: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paterson, Andrew H -- Bowers, John E -- Bruggmann, Remy -- Dubchak, Inna -- Grimwood, Jane -- Gundlach, Heidrun -- Haberer, Georg -- Hellsten, Uffe -- Mitros, Therese -- Poliakov, Alexander -- Schmutz, Jeremy -- Spannagl, Manuel -- Tang, Haibao -- Wang, Xiyin -- Wicker, Thomas -- Bharti, Arvind K -- Chapman, Jarrod -- Feltus, F Alex -- Gowik, Udo -- Grigoriev, Igor V -- Lyons, Eric -- Maher, Christopher A -- Martis, Mihaela -- Narechania, Apurva -- Otillar, Robert P -- Penning, Bryan W -- Salamov, Asaf A -- Wang, Yu -- Zhang, Lifang -- Carpita, Nicholas C -- Freeling, Michael -- Gingle, Alan R -- Hash, C Thomas -- Keller, Beat -- Klein, Patricia -- Kresovich, Stephen -- McCann, Maureen C -- Ming, Ray -- Peterson, Daniel G -- Mehboob-ur-Rahman -- Ware, Doreen -- Westhoff, Peter -- Mayer, Klaus F X -- Messing, Joachim -- Rokhsar, Daniel S -- England -- Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA. paterson@uga.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19189423" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Chromosomes, Plant/genetics ; *Evolution, Molecular ; Gene Duplication ; Genes, Plant ; Genome, Plant/*genetics ; Oryza/genetics ; Poaceae/*genetics ; Populus/genetics ; Recombination, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Deletion/genetics ; Sorghum/*genetics ; Zea mays/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-09-02
    Description: Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tyler, Brett M -- Tripathy, Sucheta -- Zhang, Xuemin -- Dehal, Paramvir -- Jiang, Rays H Y -- Aerts, Andrea -- Arredondo, Felipe D -- Baxter, Laura -- Bensasson, Douda -- Beynon, Jim L -- Chapman, Jarrod -- Damasceno, Cynthia M B -- Dorrance, Anne E -- Dou, Daolong -- Dickerman, Allan W -- Dubchak, Inna L -- Garbelotto, Matteo -- Gijzen, Mark -- Gordon, Stuart G -- Govers, Francine -- Grunwald, Niklaus J -- Huang, Wayne -- Ivors, Kelly L -- Jones, Richard W -- Kamoun, Sophien -- Krampis, Konstantinos -- Lamour, Kurt H -- Lee, Mi-Kyung -- McDonald, W Hayes -- Medina, Monica -- Meijer, Harold J G -- Nordberg, Eric K -- Maclean, Donald J -- Ospina-Giraldo, Manuel D -- Morris, Paul F -- Phuntumart, Vipaporn -- Putnam, Nicholas H -- Rash, Sam -- Rose, Jocelyn K C -- Sakihama, Yasuko -- Salamov, Asaf A -- Savidor, Alon -- Scheuring, Chantel F -- Smith, Brian M -- Sobral, Bruno W S -- Terry, Astrid -- Torto-Alalibo, Trudy A -- Win, Joe -- Xu, Zhanyou -- Zhang, Hongbin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Boore, Jeffrey L -- BB/C509123/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1261-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. bmtyler@vt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946064" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/genetics/physiology ; *Biological Evolution ; DNA, Algal/*genetics ; Genes ; *Genome ; Hydrolases/genetics/metabolism ; Photosynthesis/genetics ; Phylogeny ; Physical Chromosome Mapping ; Phytophthora/classification/*genetics/*pathogenicity/physiology ; Plant Diseases/microbiology ; Polymorphism, Single Nucleotide ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Symbiosis ; Toxins, Biological/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    The Chlamydomonas genome reveals the evolution of key animal and plant functions (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-13
    Description: Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the approximately 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Merchant, Sabeeha S -- Prochnik, Simon E -- Vallon, Olivier -- Harris, Elizabeth H -- Karpowicz, Steven J -- Witman, George B -- Terry, Astrid -- Salamov, Asaf -- Fritz-Laylin, Lillian K -- Marechal-Drouard, Laurence -- Marshall, Wallace F -- Qu, Liang-Hu -- Nelson, David R -- Sanderfoot, Anton A -- Spalding, Martin H -- Kapitonov, Vladimir V -- Ren, Qinghu -- Ferris, Patrick -- Lindquist, Erika -- Shapiro, Harris -- Lucas, Susan M -- Grimwood, Jane -- Schmutz, Jeremy -- Cardol, Pierre -- Cerutti, Heriberto -- Chanfreau, Guillaume -- Chen, Chun-Long -- Cognat, Valerie -- Croft, Martin T -- Dent, Rachel -- Dutcher, Susan -- Fernandez, Emilio -- Fukuzawa, Hideya -- Gonzalez-Ballester, David -- Gonzalez-Halphen, Diego -- Hallmann, Armin -- Hanikenne, Marc -- Hippler, Michael -- Inwood, William -- Jabbari, Kamel -- Kalanon, Ming -- Kuras, Richard -- Lefebvre, Paul A -- Lemaire, Stephane D -- Lobanov, Alexey V -- Lohr, Martin -- Manuell, Andrea -- Meier, Iris -- Mets, Laurens -- Mittag, Maria -- Mittelmeier, Telsa -- Moroney, James V -- Moseley, Jeffrey -- Napoli, Carolyn -- Nedelcu, Aurora M -- Niyogi, Krishna -- Novoselov, Sergey V -- Paulsen, Ian T -- Pazour, Greg -- Purton, Saul -- Ral, Jean-Philippe -- Riano-Pachon, Diego Mauricio -- Riekhof, Wayne -- Rymarquis, Linda -- Schroda, Michael -- Stern, David -- Umen, James -- Willows, Robert -- Wilson, Nedra -- Zimmer, Sara Lana -- Allmer, Jens -- Balk, Janneke -- Bisova, Katerina -- Chen, Chong-Jian -- Elias, Marek -- Gendler, Karla -- Hauser, Charles -- Lamb, Mary Rose -- Ledford, Heidi -- Long, Joanne C -- Minagawa, Jun -- Page, M Dudley -- Pan, Junmin -- Pootakham, Wirulda -- Roje, Sanja -- Rose, Annkatrin -- Stahlberg, Eric -- Terauchi, Aimee M -- Yang, Pinfen -- Ball, Steven -- Bowler, Chris -- Dieckmann, Carol L -- Gladyshev, Vadim N -- Green, Pamela -- Jorgensen, Richard -- Mayfield, Stephen -- Mueller-Roeber, Bernd -- Rajamani, Sathish -- Sayre, Richard T -- Brokstein, Peter -- Dubchak, Inna -- Goodstein, David -- Hornick, Leila -- Huang, Y Wayne -- Jhaveri, Jinal -- Luo, Yigong -- Martinez, Diego -- Ngau, Wing Chi Abby -- Otillar, Bobby -- Poliakov, Alexander -- Porter, Aaron -- Szajkowski, Lukasz -- Werner, Gregory -- Zhou, Kemin -- Grigoriev, Igor V -- Rokhsar, Daniel S -- Grossman, Arthur R -- GM07185/GM/NIGMS NIH HHS/ -- GM42143/GM/NIGMS NIH HHS/ -- R01 GM032843/GM/NIGMS NIH HHS/ -- R01 GM042143/GM/NIGMS NIH HHS/ -- R01 GM042143-09/GM/NIGMS NIH HHS/ -- R01 GM060992/GM/NIGMS NIH HHS/ -- R01 GM062915-06/GM/NIGMS NIH HHS/ -- R37 GM030626/GM/NIGMS NIH HHS/ -- R37 GM042143/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):245-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932292" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/*genetics/*physiology ; Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*genetics/physiology ; Chloroplasts/metabolism ; Computational Biology ; DNA, Algal/genetics ; Flagella/metabolism ; Genes ; *Genome ; Genomics ; Membrane Transport Proteins/genetics/physiology ; Molecular Sequence Data ; Multigene Family ; Photosynthesis/genetics ; Phylogeny ; Plants/genetics ; Proteome ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-07
    Description: Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Putnam, Nicholas H -- Srivastava, Mansi -- Hellsten, Uffe -- Dirks, Bill -- Chapman, Jarrod -- Salamov, Asaf -- Terry, Astrid -- Shapiro, Harris -- Lindquist, Erika -- Kapitonov, Vladimir V -- Jurka, Jerzy -- Genikhovich, Grigory -- Grigoriev, Igor V -- Lucas, Susan M -- Steele, Robert E -- Finnerty, John R -- Technau, Ulrich -- Martindale, Mark Q -- Rokhsar, Daniel S -- 5 P41 LM006252-09/LM/NLM NIH HHS/ -- THL007279F/PHS HHS/ -- New York, N.Y. -- Science. 2007 Jul 6;317(5834):86-94.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17615350" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Cell Adhesion ; Evolution, Molecular ; Genes ; Genetic Linkage ; *Genome ; Genome, Human ; Genomics ; Humans ; Introns ; Metabolic Networks and Pathways ; Multigene Family ; Muscles/physiology ; Nervous System Physiological Phenomena ; Phylogeny ; Sea Anemones/*genetics/metabolism ; Sequence Analysis, DNA ; Signal Transduction ; Synteny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007
    Description: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rensing, Stefan A -- Lang, Daniel -- Zimmer, Andreas D -- Terry, Astrid -- Salamov, Asaf -- Shapiro, Harris -- Nishiyama, Tomoaki -- Perroud, Pierre-Francois -- Lindquist, Erika A -- Kamisugi, Yasuko -- Tanahashi, Takako -- Sakakibara, Keiko -- Fujita, Tomomichi -- Oishi, Kazuko -- Shin-I, Tadasu -- Kuroki, Yoko -- Toyoda, Atsushi -- Suzuki, Yutaka -- Hashimoto, Shin-Ichi -- Yamaguchi, Kazuo -- Sugano, Sumio -- Kohara, Yuji -- Fujiyama, Asao -- Anterola, Aldwin -- Aoki, Setsuyuki -- Ashton, Neil -- Barbazuk, W Brad -- Barker, Elizabeth -- Bennetzen, Jeffrey L -- Blankenship, Robert -- Cho, Sung Hyun -- Dutcher, Susan K -- Estelle, Mark -- Fawcett, Jeffrey A -- Gundlach, Heidrun -- Hanada, Kousuke -- Heyl, Alexander -- Hicks, Karen A -- Hughes, Jon -- Lohr, Martin -- Mayer, Klaus -- Melkozernov, Alexander -- Murata, Takashi -- Nelson, David R -- Pils, Birgit -- Prigge, Michael -- Reiss, Bernd -- Renner, Tanya -- Rombauts, Stephane -- Rushton, Paul J -- Sanderfoot, Anton -- Schween, Gabriele -- Shiu, Shin-Han -- Stueber, Kurt -- Theodoulou, Frederica L -- Tu, Hank -- Van de Peer, Yves -- Verrier, Paul J -- Waters, Elizabeth -- Wood, Andrew -- Yang, Lixing -- Cove, David -- Cuming, Andrew C -- Hasebe, Mitsuyasu -- Lucas, Susan -- Mishler, Brent D -- Reski, Ralf -- Grigoriev, Igor V -- Quatrano, Ralph S -- Boore, Jeffrey L -- BBS/E/C/00004948/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079367" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Angiosperms/genetics/physiology ; Animals ; Arabidopsis/genetics/physiology ; *Biological Evolution ; Bryopsida/*genetics/physiology ; Chlamydomonas reinhardtii/genetics/physiology ; Computational Biology ; DNA Repair ; Dehydration ; Gene Duplication ; Genes, Plant ; *Genome, Plant ; Metabolic Networks and Pathways/genetics ; Multigene Family ; Oryza/genetics/physiology ; Phylogeny ; Plant Proteins/genetics/physiology ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Sequence Analysis, DNA ; Signal Transduction/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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