The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Type Article
Date 2008-11
Language English
Author(s) Bowler C1, 2, Allen A1, 3, Badger J3, Grimwood J4, Jabbari K1, Kuo A5, Maheswari U1, Martens C6, Maumus F1, Otillar R5, Rayko E1, Salamov A5, Vandepoele K6, Beszteri B7, Gruber A8, Heijde M1, Katinka M9, Mock T10, Valentin K7, Verret F11, Berges J12, Brownlee C11, Cadoret Jean-Paul13, Chiovitti A14, Choi C12, Coesel S2, De Martino A1, Detter J5, Durkin C10, Falciatore A2, Fournet J15, Haruta M16, Huysman M6, 17, Jenkins B18, 19, Jiroutova K20, 21, Jorgensen R22, 23, Joubert Y15, Kaplan A24, Kroger N25, 26, 27, Kroth P8, La Roche J28, Lindquist E5, Lommer M28, Martin Jezequel V15, Lopez P1, Lucas S5, Mangogna M2, McGinnis K22, 23, Medlin L7, 11, Montsant A1, 2, Oudot Le Secq M29, Napoli C22, 23, Obornik M20, 21, Parker M10, Petit J9, Porcel B9, Poulsen N30, Robison M16, Rychlewski L31, Rynearson T32, Schmutz J4, Shapiro H5, Siaut M2, Stanley M33, Sussman M16, Taylor A11, 34, Vardi A1, 35, Von Dassow P36, Vyverman W17, Willis A14, Wyrwicz L31, Rokhsar D5, Weissenbach J9, Armbrust E10, Green B29, Van De Peer Y6, Grigoriev Iv 5
Affiliation(s) 1 : Ecole Normale Super, CNRS, Dept Biol, UMR8186, F-75005 Paris, France.
2 : Stn Zool A Dohrn, I-80121 Naples, Italy.
3 : J Craig Venter Inst, San Diego, CA 92121 USA.
4 : Stanford Human Genome Ctr, Joint Genome Inst Stanford, Palo Alto, CA 94304 USA.
5 : Joint Genome Inst, Walnut Creek, CA 94598 USA.
6 : Univ Ghent VIB, Dept Plant Syst Biol, B-9052 Ghent, Belgium.
7 : Alfred Wegener Inst Polar & Marine Res, D-27570 Bremerhaven, Germany.
8 : Univ Konstanz, Fachbereich Biol, D-78457 Constance, Germany.
9 : CNRS, CEA Inst Genom, UMR 8030, F-91057 Evry, France.
10 : Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.
11 : Marine Biol Assoc United Kingdom Lab, Plymouth PL1 2PB, Devon, England.
12 : Univ Wisconsin, Dept Biol Sci, Milwaukee, WI 53201 USA.
13 : IFREMER, PBA, F-44311 Nantes 03, France.
14 : Univ Melbourne, Sch Bot, Melbourne, Vic 3010, Australia.
15 : Univ Nantes, Lab Mer Mol Sante, Fac Tech Sci, EA 2160, F-44322 Nantes 3, France.
16 : Univ Wisconsin, Ctr Biotechnol, Madison, WI 53706 USA.
17 : Univ Ghent, Lab Protistol & Aquat Ecol, B-9000 Ghent, Belgium.
18 : Univ Rhode Isl, Dept Cell & Mol Biol, Kingston, RI 02881 USA.
19 : Univ Rhode Isl, Grad Sch Oceanog, Kingston, RI 02881 USA.
20 : Acad Sci Czech Republic, Inst Parasitol, Ctr Biol, CR-37005 Ceske Budejovice, Czech Republic.
21 : Univ S Bohemia, Fac Sci, CR-37005 Ceske Budejovice, Czech Republic.
22 : Univ Arizona, Bio5 Inst, Tucson, AZ 85719 USA.
23 : Univ Arizona, Dept Plant Sci, Tucson, AZ 85719 USA.
24 : Hebrew Univ Jerusalem, Dept Plant & Environm Sci, IL-91904 Jerusalem, Israel.
25 : Georgia Inst Technol, Sch Chem & Biochem, Atlanta, GA 30332 USA.
26 : Georgia Inst Technol, Sch Mat Sci & Engn, Atlanta, GA 30332 USA.
27 : Georgia Inst Technol, Sch Biol, Atlanta, GA 30332 USA.
28 : Leibniz Inst Marine Sci, D-24105 Kiel, Germany.
29 : Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
30 : Georgia Inst Technol, Sch Chem & Biochem, Atlanta, GA 30332 USA.
31 : BioInfoBank Inst, PL-60744 Poznan, Poland.
32 : Univ Rhode Isl, Grad Sch Oceanog, Narragansett, RI 02882 USA.
33 : Dunstaffnage Marine Res Lab, Scottish Assoc Marine Sci, Oban PA37 1QA, Argyll, Scotland.
34 : Univ N Carolina, Dept Biol & Marine Biol, Wilmington, NC 28403 USA.
35 : Rutgers State Univ, Inst Marine & Coastal Sci, Environm Biophys & Mol Ecol Grp, New Brunswick, NJ 08901 USA.
36 : CNRS, Biol Stn, UMR7144, F-29682 Roscoff, France.
Source Nature (0028-0836) (Nature), 2008-11 , Vol. 456 , N. 7219 , P. 239-244
DOI 10.1038/nature07410
WOS© Times Cited 961
Abstract 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(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). 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 (similar to 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.
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Bowler C, Allen A, Badger J, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar R, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges J, Brownlee C, Cadoret Jean-Paul, Chiovitti A, Choi C, Coesel S, De Martino A, Detter J, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman M, Jenkins B, Jiroutova K, Jorgensen R, Joubert Y, Kaplan A, Kroger N, Kroth P, La Roche J, Lindquist E, Lommer M, Martin Jezequel V, Lopez P, Lucas S, Mangogna M, McGinnis K, Medlin L, Montsant A, Oudot Le Secq M, Napoli C, Obornik M, Parker M, Petit J, Porcel B, Poulsen N, Robison M, Rychlewski L, Rynearson T, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman M, Taylor A, Vardi A, Von Dassow P, Vyverman W, Willis A, Wyrwicz L, Rokhsar D, Weissenbach J, Armbrust E, Green B, Van De Peer Y, Grigoriev Iv (2008). The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature, 456(7219), 239-244. Publisher's official version : https://doi.org/10.1038/nature07410 , Open Access version : https://archimer.ifremer.fr/doc/00000/4809/