Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF: Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 1998, 8: 464-478.
CAS
PubMed
Google Scholar
Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE: The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2002, 3: RESEARCH0084-10.1186/gb-2002-3-12-research0084.
Article
PubMed Central
PubMed
Google Scholar
Kapitonov VV, Jurka J: Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci USA. 2003, 100: 6569-6574. 10.1073/pnas.0732024100.
Article
PubMed Central
CAS
PubMed
Google Scholar
Quesneville H, Nouaud D, Anxolabehere D: Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes. J Mol Evol. 2003, 57 (Suppl 1): S50-59. 10.1007/s00239-003-0007-2.
Article
CAS
PubMed
Google Scholar
Smit AF: Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999, 9: 657-663. 10.1016/S0959-437X(99)00031-3.
Article
CAS
PubMed
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062.
Article
CAS
PubMed
Google Scholar
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL: The paleontology of intergene retrotransposons of maize. Nat Genet. 1998, 20: 43-45. 10.1038/1695.
Article
CAS
PubMed
Google Scholar
SanMiguel P, Tikhonov A, Jin JK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL: Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996, 274: 765-768. 10.1126/science.274.5288.765.
Article
CAS
PubMed
Google Scholar
Kumar A, Bennetzen JL: Plant retrotransposons. Annu Rev Genet. 1999, 33: 479-532. 10.1146/annurev.genet.33.1.479.
Article
CAS
PubMed
Google Scholar
Xiong Y, Eickbush TH: Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990, 9: 3353-3362.
PubMed Central
CAS
PubMed
Google Scholar
Round FE, Crawford RM, Mann DG: The Diatoms Biology and Morphology of the Genera. 1990, London, UK: Cambridge University Press
Google Scholar
Nelson DM, Treguer P, Brzezinski MA, Leynaert A, Queguiner B: Production and dissolution of biogenic silica in the ocean - Revised global estimates, comparison with regional data and relationship to biogenic sedimentation. Global Biogeochemical Cycles. 1995, 9: 359-372. 10.1029/95GB01070.
Article
CAS
Google Scholar
Raven JA, Waite AM: The evolution of silicification in diatoms: inescapable sinking and sinking as escape?. New Phytologist. 2004, 162: 45-61. 10.1111/j.1469-8137.2004.01022.x.
Article
Google Scholar
Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O, Taylor FJ: The evolution of modern eukaryotic phytoplankton. Science. 2004, 305: 354-360. 10.1126/science.1095964.
Article
CAS
PubMed
Google Scholar
Armbrust V, Berges J, Bowler C, Green B, Martinez D, Putnam N, Zhou S, Allenn A, Apt K, Bechner M, Brzezinski M, Chaal B, Chiovitti A, Davis A, Demarest M, Detter C, Glavina T, Goodstein D, Hadi M, Hellsten U, Hildebrand M, Jenkins B, Jurka J, Kapitonov V, Kroger N, Lau W, Lane T, Larimer F, Lippmeier C, Lucas S: The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism. Science. 2004, 306: 79-86. 10.1126/science.1101156.
Article
CAS
PubMed
Google Scholar
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A: The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008, 456: 239-244. 10.1038/nature07410.
Article
CAS
PubMed
Google Scholar
Kapitonov VV, Jurka J: Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA Cell Biol. 2004, 23: 311-324. 10.1089/104454904323090949.
Article
CAS
PubMed
Google Scholar
Smit AFA, Hubley R, Green P: RepeatMasker Open-3.0. 1996, [http://www.repeatmasker.org]
Google Scholar
Maheswari U, Mock T, Armbrust EV, Bowler C: Update of the Diatom EST Database a new tool for digital transcriptomics. Nucleic Acids Res. 2009, D1001-5. 10.1093/nar/gkn905. Epub 2008 Nov 23, 37 Database
Pouteau S, Hunter E, Grandbastien MA, Caboche M: Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J. 1991, 10: 1911-1918.
PubMed Central
CAS
PubMed
Google Scholar
Servant G, Pennetier C, Lesage P: Remodeling yeast gene transcription by activating the Ty1 long terminal repeat retrotransposon under severe adenine deficiency. Mol Cell Biol. 2008, 28: 5543-5554. 10.1128/MCB.00416-08.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chandler VL, Walbot V: DNA modification of a maize transposable element correlates with loss of activity. Proc Natl Acad Sci USA. 1986, 83: 1767-1771. 10.1073/pnas.83.6.1767.
Article
PubMed Central
CAS
PubMed
Google Scholar
Scortecci KC, Dessaux Y, Van Sluys MA: Somatic excision of the Ac transposable element in transgenic Arabidopsis thaliana after 5-azacytidine treatment. Plant Cell Physiol. 1997, 38: 336-343.
Article
CAS
PubMed
Google Scholar
Miura A, Watanabe S, Toyama T, Shmada H, Kakutani T: Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature. 2001, 411: 212-214. 10.1038/35075612.
Article
CAS
PubMed
Google Scholar
Liu ZL, Han FP, Tan M, Shan XH, Dong YZ, Wang XZ, Fedak G, Hao S, Liu B: Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theor Appl Genet. 2004, 109: 200-209. 10.1007/s00122-004-1618-8.
Article
CAS
PubMed
Google Scholar
Hashida SN, Uchiyama T, Martin C, Kishima Y, Sano Y, Mikami T: The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. Plant Cell. 2006, 18: 104-118. 10.1105/tpc.105.037655.
Article
PubMed Central
CAS
PubMed
Google Scholar
De Martino A, Meichenin A, Pan KH, Bowler C: Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions. Journal of Phycology. 2007, 43: 992-1009. 10.1111/j.1529-8817.2007.00384.x.
Article
CAS
Google Scholar
Devos KM, Brown JK, Bennetzen JL: Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 2002, 12: 1075-1079. 10.1101/gr.132102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO: Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004, 304: 66-74. 10.1126/science.1093857.
Article
CAS
PubMed
Google Scholar
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S: The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007, 5: e77-10.1371/journal.pbio.0050077.
Article
PubMed Central
PubMed
Google Scholar
Peddigari S, Zhang W, Takechi K, Takano H, Takio S: Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis. Gene. 2008, 424: 153-158. 10.1016/j.gene.2008.07.021.
Article
CAS
PubMed
Google Scholar
Terrat Y, Bonnivard E, Higuet D: GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species. Mol Genet Genomics. 2008, 279: 63-73. 10.1007/s00438-007-0295-0.
Article
CAS
PubMed
Google Scholar
Piganeau G, Desdevises Y, Derelle E, Moreau H: Picoeukaryotic sequences in the Sargasso Sea metagenome. Genome Biol. 2008, 9: R5-10.1186/gb-2008-9-1-r5.
Article
PubMed Central
PubMed
Google Scholar
Grandbastien MA, Spielmann A, Caboche M: Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature. 1989, 337: 376-380. 10.1038/337376a0.
Article
CAS
PubMed
Google Scholar
Bennetzen JL, Kellogg EA: Do Plants Have a One-Way Ticket to Genomic Obesity?. The Plant cell. 1997, 9: 1509-1514. 10.2307/3870439.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AE: Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum. Plant Cell. 1999, 11: 1769-1784. 10.1105/tpc.11.9.1769.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wessler SR: Turned on by stress. Plant retrotransposons. Curr Biol. 1996, 6: 959-961. 10.1016/S0960-9822(02)00638-3.
Article
CAS
PubMed
Google Scholar
Kalender R, Tanskanen J, Immonen S, Nevo E, Schulman AE: Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA. 2000, 97: 6603-6607. 10.1073/pnas.110587497.
Article
Google Scholar
Falkowski PG: Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature. 1997, 387: 272-275. 10.1038/387272a0.
Article
CAS
Google Scholar
Smetacek V: Diatoms and the ocean carbon cycle. Protist. 1999, 150: 25-32. 10.1016/S1434-4610(99)70006-4.
Article
CAS
PubMed
Google Scholar
Vardi A, Bidle KD, Kwityn C, Hirsh DJ, Thompson SM, Callow JA, Falkowski P, Bowler C: A diatom gene regulating nitric-oxide signaling and susceptibility to diatom-derived aldehydes. Curr Biol. 2008, 18: 895-899. 10.1016/j.cub.2008.05.037.
Article
CAS
PubMed
Google Scholar
Vardi A, Formiggini F, Casotti R, De Martino A, Ribalet F, Miralto A, Bowler C: A stress surveillance system based on calcium and nitric oxide in marine diatoms. PLoS Biol. 2006, 4: e60-10.1371/journal.pbio.0040060.
Article
PubMed Central
PubMed
Google Scholar
Ianora A, Miralto A, Poulet SA, Carotenuto Y, Buttino I, Romano G, Casotti R, Pohnert G, Wichard T, Colucci-D'Amato L, Terrazzano G, Smetacek V: Aldehyde suppression of copepod recruitment in blooms of a ubiquitous planktonic diatom. Nature. 2004, 429: 403-407. 10.1038/nature02526.
Article
CAS
PubMed
Google Scholar
Fontana A, d'Ippolito G, Cutignano A, Romano G, Lamari N, Gallucci AM, Cimino G, Miralto A, Ianora A: LOX-induced lipid peroxidation mechanism responsible for the detrimental effect of marine diatoms on Zooplankton grazers. Chembiochem. 2007, 8: 1810-1818. 10.1002/cbic.200700269.
Article
CAS
PubMed
Google Scholar
Ribalet F, Berges JA, Ianora A, Casotti R: Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes. Aquatic Toxicology. 2007, 85: 219-227. 10.1016/j.aquatox.2007.09.006.
Article
CAS
PubMed
Google Scholar
Ribalet F, Wichard T, Pohnert G, Ianora A, Miralto A, Casotti R: Age and nutrient limitation enhance polyunsaturated aldehyde production in marine diatoms. Phytochemistry. 2007, 68: 2059-2067. 10.1016/j.phytochem.2007.05.012.
Article
CAS
PubMed
Google Scholar
Casotti R, Mazza S, Brunet C, Vantrepotte V, Ianora A, Miralto A: Growth inhibition and toxicity of the diatom aldehyde 2-trans, 4-trans-decadienal on Thalassiosira weissflogii (Bacillariophyceae). Journal of Phycology. 2005, 41: 7-20. 10.1111/j.1529-8817.2005.04052.x.
Article
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.
Article
CAS
PubMed
Google Scholar
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005, 110: 462-467. 10.1159/000084979.
Article
CAS
PubMed
Google Scholar
Krell A, Gloeckner G: Analysis of an osmotic stress induced cDNA library of the psychrophilic diatom Fragilariopsis cylindrus. Public EST library deposited at NCBI in. 2004
Google Scholar
Higgins DG, Sharp PM: CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1998, 73: 237-244. 10.1016/0378-1119(88)90330-7.
Article
Google Scholar
Nei M, Chakraborty R: Empirical relationship between the number of nucleotide substitutions and interspecific identity of amino acid sequences in some proteins. J Mol Evol. 1976, 7: 313-323. 10.1007/BF01743627.
Article
CAS
PubMed
Google Scholar
Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987, 4: 406-425.
CAS
PubMed
Google Scholar
Kumar S, Tamura K, Nei M: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004, 5: 150-163. 10.1093/bib/5.2.150.
Article
CAS
PubMed
Google Scholar
Huson DH, Bryant D: Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006, 23: 254-267. 10.1093/molbev/msj030.
Article
CAS
PubMed
Google Scholar
Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF: Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA. 2003, 9: 1422-1430. 10.1261/rna.5105503.
Article
PubMed Central
CAS
PubMed
Google Scholar
Toh H, Hayashida H, Miyata T: Sequence homology between retroviral reverse transcriptase and putative polymerases of hepatitis B virus and cauliflower mosaic virus. Nature. 1983, 305: 827-829. 10.1038/305827a0.
Article
CAS
PubMed
Google Scholar
Toh H, Kikuno R, Hayashida H, Miyata T, Kugimiya W, Inouye S, Yuki S, Saigo K: Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus. EMBO J. 1985, 4: 1267-1272.
PubMed Central
CAS
PubMed
Google Scholar
Guillard RRL: Culture of phytoplankton for feeding marine invertebrates. Culture of Marine Invertebrate Animals. Edited by: Smith WLaCMH. 1975, New York, USA: Plenum Press
Google Scholar
Andersen RA, Morton S, Sexton J: CCMP - Provasoli-Guillard National Center for Culture of Marine Phytoplankton 1997 list of strains. Journal of Phycology. 1997, 33 (suppl): 1-75. 10.1111/j.0022-3646.1997.00001.x.
Article
Google Scholar
Petit M, Lim KY, Julio E, Poncet C, Dorlhac de Borne F, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C: Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Mol Genet Genomics. 2007, 278: 1-15. 10.1007/s00438-007-0226-0.
Article
CAS
PubMed
Google Scholar
Siaut M, Heijde M, Mangogna M, Montsant A, Coesel S, Allen A, Manfredonia A, Falciatore A, Bowler C: Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene. 2007, 406: 23-35.
Article
CAS
PubMed
Google Scholar
Falciatore A, Casotti R, Leblanc C, Abrescia C, Bowler C: Transformation of Nonselectable Reporter Genes in Marine Diatoms. Mar Biotechnol (NY). 1999, 1: 239-251. 10.1007/PL00011773.
Article
CAS
Google Scholar
Jefferson RA, Kavanagh TA, Bevan MW: GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 1987, 6: 3901-3907.
PubMed Central
CAS
PubMed
Google Scholar