algal dna

Summary

Summary: Deoxyribonucleic acid that makes up the genetic material of algae.

Top Publications

  1. Bowler C, Allen A, Badger J, Grimwood J, Jabbari K, Kuo A, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008;456:239-44 pubmed publisher
    ..These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans. ..
  2. Rynearson T, Lin E, Armbrust E. Metapopulation Structure in the Planktonic Diatom Ditylum brightwellii (Bacillariophyceae). Protist. 2009;160:111-21 pubmed publisher
  3. Jiang R, Tyler B, Whisson S, Hardham A, Govers F. Ancient origin of elicitin gene clusters in Phytophthora genomes. Mol Biol Evol. 2006;23:338-51 pubmed
    ..Overall, eli and ell genes are expressed at different levels and in different life cycle stages but those sharing the same phylogenetic clade appear to have similar expression patterns. ..
  4. Tyler B, Tripathy S, Zhang X, Dehal P, Jiang R, Aerts A, et al. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science. 2006;313:1261-6 pubmed
  5. Smith D, Lee R. Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis. BMC Evol Biol. 2009;9:120 pubmed publisher
  6. Wang Y, Joly S, Morse D. Phylogeny of dinoflagellate plastid genes recently transferred to the nucleus supports a common ancestry with red algal plastid genes. J Mol Evol. 2008;66:175-84 pubmed publisher
  7. Kai A, Yoshii Y, Nakayama T, Inouye I. Aurearenophyceae classis nova, a new class of Heterokontophyta based on a new marine unicellular alga Aurearena cruciata gen. et sp. nov. inhabiting sandy beaches. Protist. 2008;159:435-57 pubmed publisher
    ..Molecular phylogenetic trees suggested that this alga was a new and independent member of the clade that included the Phaeophyceae and Xanthophyceae (PX clade). A new class, Aurearenophyceae classis nova was proposed for A. cruciata. ..
  8. Nakada T, Misawa K, Nozaki H. Molecular systematics of Volvocales (Chlorophyceae, Chlorophyta) based on exhaustive 18S rRNA phylogenetic analyses. Mol Phylogenet Evol. 2008;48:281-91 pubmed publisher
    ..Phylogenetic classification following PhyloCode was proposed based on the presented 18S rRNA gene phylogeny along with the results of previous combined 18S and 26S rRNA and chloroplast multigene analyses. ..
  9. Cheung F, Win J, Lang J, Hamilton J, Vuong H, Leach J, et al. Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches. BMC Genomics. 2008;9:542 pubmed publisher
    ..95) using two high throughput sequencing methods, Sanger-based chain termination sequencing and pyrosequencing-based sequencing-by-synthesis...

More Information

Publications62

  1. Smith D, Lee R. The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA. BMC Genomics. 2009;10:132 pubmed publisher
    ..carteri draft nuclear genome sequence...
  2. Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van de Peer Y. The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Mol Biol Evol. 2007;24:956-68 pubmed
    ..Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta. ..
  3. Hauth A, Maier U, Lang B, Burger G. The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region. Nucleic Acids Res. 2005;33:4433-42 pubmed
  4. Randall T, Dwyer R, Huitema E, Beyer K, Cvitanich C, Kelkar H, et al. Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Mol Plant Microbe Interact. 2005;18:229-43 pubmed
  5. Merchant S, Prochnik S, Vallon O, Harris E, Karpowicz S, Witman G, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007;318:245-50 pubmed
  6. Sato N. [Structure, replication and dynamism of chloroplast nucleoids]. Tanpakushitsu Kakusan Koso. 2005;50:1838-42 pubmed
  7. McLeod A, Botha W, Meitz J, Spies C, Tewoldemedhin Y, Mostert L. Morphological and phylogenetic analyses of Pythium species in South Africa. Mycol Res. 2009;113:933-51 pubmed publisher
    ..Additionally, three isolates (PPRI 8428, 8300 and 8418) were identified that may each represent putative new species, Pythium sp. WJB-1 to WJB-3...
  8. Wang N, Sherwood A, Kurihara A, Conklin K, Sauvage T, Presting G. The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data. BMC Plant Biol. 2009;9:117 pubmed publisher
    ..It is publicly available at http://algae.manoa.hawaii.edu. ..
  9. Berdoulay M, Salvado J. Genetic characterization of microbial communities living at the surface of building stones. Lett Appl Microbiol. 2009;49:311-6 pubmed publisher
    ..The easy-to-run molecular method described here has practical importance to establish microbiological diagnosis and to define strategies for protection and restoration of stone surfaces. ..
  10. Gamby J, Lazerges M, Girault H, Deslouis C, Gabrielli C, Perrot H, et al. Electroacoustic polymer microchip as an alternative to quartz crystal microbalance for biosensor development. Anal Chem. 2008;80:8900-7 pubmed publisher
    ..The electroacoustic PET device, approximately 100 times smaller than a microbalance quartz crystal, is interesting for the large-scale integration of acoustic sensors in biochips. ..
  11. de los Rios A, Sancho L, Grube M, Wierzchos J, Ascaso C. Endolithic growth of two Lecidea lichens in granite from continental Antarctica detected by molecular and microscopy techniques. New Phytol. 2005;165:181-89 pubmed
    ..The combined approach proposed is useful for mapping the distribution of endolithic lichens and analysing the processes that occur in their microscopic environment. ..
  12. Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre J, Gourgues M. Cellular and molecular characterization of Phytophthora parasitica appressorium-mediated penetration. New Phytol. 2010;185:248-57 pubmed publisher
    ..parasitica infection provided us with an unprecedented opportunity to decipher the molecular mechanisms involved in penetration of the plant cells during the initiation of infection by a soil-borne oomycete. ..
  13. Rybalka N, Andersen R, Kostikov I, Mohr K, Massalski A, Olech M, et al. Testing for endemism, genotypic diversity and species concepts in Antarctic terrestrial microalgae of the Tribonemataceae (Stramenopiles, Xanthophyceae). Environ Microbiol. 2009;11:554-65 pubmed publisher
    ..Fortunately, the presence of distinctive sequence regions within the psbA/rbcL spacer, together with differences in the rbcL phylogeny, provided significant autoapomorphic criteria to re-define the Tribonemataceae species. ..
  14. Lins de Barros M, Vieira R, Cardoso A, Monteiro V, Turque A, Silveira C, et al. Archaea, Bacteria, and algal plastids associated with the reef-building corals Siderastrea stellata and Mussismilia hispida from Búzios, South Atlantic Ocean, Brazil. Microb Ecol. 2010;59:523-32 pubmed publisher
    ..Our data improves the pool of available information on Brazilian coral microbes and shows corals as sources of diverse prokaryotic and picoeukaryotic communities. ..
  15. Monnier A, Liverani S, Bouvet R, Jesson B, Smith J, Mosser J, et al. Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles. BMC Genomics. 2010;11:192 pubmed publisher
    ..tauri to grow under a wide range of light intensities. ..
  16. Nakada T, Nozaki H, Tomita M. Another origin of coloniality in volvocaleans: the phylogenetic position of Pyrobotrys arnoldi (Spondylomoraceae, Volvocales). J Eukaryot Microbiol. 2010;57:379-82 pubmed publisher
    ..The results indicate that colony formation of Spondylomoraceae independently evolved from unicellular volvocaleans. The phylogenetic position of problematic "Pascherina tetras" SAG 159-1 was also analyzed. ..
  17. Cheang C, Chu K, Ang P. Phylogeography of the marine macroalga Sargassum hemiphyllum (Phaeophyceae, Heterokontophyta) in northwestern Pacific. Mol Ecol. 2010;19:2933-48 pubmed publisher
    ..hemiphyllum is highly probable as all these individuals share a pool of nuclear ITS2 sequences, possibly attributable to incomplete concerted evolution of ITS2. ..
  18. Chavarriaga D, Bodles W, Leifert C, Belbahri L, Woodward S. Phytophthora cinnamomi and other fine root pathogens in north temperate pine forests. FEMS Microbiol Lett. 2007;276:67-74 pubmed
    ..ultimum and Fusarium sp., or by the Fusarium isolate alone. These nonspecific pathogens may persist on the roots of understorey and herbaceous plants in the pine forests. ..
  19. Supabandhu J, Fisher M, Mendoza L, Vanittanakom N. Isolation and identification of the human pathogen Pythium insidiosum from environmental samples collected in Thai agricultural areas. Med Mycol. 2008;46:41-52 pubmed
    ..insidiosum infection for individuals working in endemic agricultural areas. ..
  20. Nozaki H, Takano H, Misumi O, Terasawa K, Matsuzaki M, Maruyama S, et al. A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae. BMC Biol. 2007;5:28 pubmed
    ..These unusually simple genomic features in the 100% complete genome sequence of C. merolae are extremely useful for further studies of eukaryotic cells. ..
  21. Lazerges M, Perrot H, Antoine E, Defontaine A, Compere C. Oligonucleotide quartz crystal microbalance sensor for the microalgae Alexandrium minutum (Dinophyceae). Biosens Bioelectron. 2006;21:1355-8 pubmed
    ..This setup constitutes a biosensor, which is sensitive and selective, and the hybridization ratio between hybridized complementary DNA and immobilized DNA probes is 47%. ..
  22. Kapraun D. Nuclear DNA content estimates in green algal lineages: chlorophyta and streptophyta. Ann Bot. 2007;99:677-701 pubmed
    ..Both mechanistic and ecological processes are discussed that could have produced the observed C-value increase of >100-fold in the charophyte green algae whereas the ancestral genome was conserved in the embryophytes. ..
  23. Su Z, Qian K, Tan C, Meng C, Qin S. Recombination and heterologous expression of allophycocyanin gene in the chloroplast of Chlamydomonas reinhardtii. Acta Biochim Biophys Sin (Shanghai). 2005;37:709-12 pubmed
    ..These findings pave the way to the reconstitution of multi-subunit proteins or metabolic pathways in transgenic C. reinhardtii chloroplasts in a single transformation event. ..
  24. Agarkova I, Dunigan D, Van Etten J. Virion-associated restriction endonucleases of chloroviruses. J Virol. 2006;80:8114-23 pubmed
    ..These immediate-early events associated with chlorovirus infections may facilitate rapid switching of the host transcriptional apparatus to viral transcription, which begins within 5 to 10 min p.i. ..
  25. Bala K, Gautam N, Paul B. Pythium rhizo-oryzae sp. nov. isolated from paddy fields: taxonomy, ITS region of rDNA, and comparison with related species. Curr Microbiol. 2006;52:102-7 pubmed
    ..Taxonomic description of this new species and its comparison with related oomycetes, together with the sequence of the PCR amplified internal transcribed region (spacers ITS1, ITS2, and the gene 5.8S) of its rDNA are given here...
  26. Vitova M, Hendrychová J, Cepak V, Zachleder V. Visualization of DNA-containing structures in various species of Chlorophyta, Rhodophyta and Cyanophyta using SYBR Green I dye. Folia Microbiol (Praha). 2005;50:333-40 pubmed
    ..Staining with SYBR Green I can be recommended as a fast, safe and efficient method for the detection of DNA-containing structures in vivo. ..
  27. Senda M, Kageyama K, Suga H, Lévesque C. Two new species of Pythium, P. senticosum and P. takayamanum,isolated from cool-temperate forest soil in Japan. Mycologia. 2009;101:439-48 pubmed
    ..P. senticosum is closely related to P. dimorphum and P. undulatum whereas P. takayamanum is closely related to P. rhizosaccharum and P. parvum. ..
  28. Aeling K, Steffen N, Johnson M, Hatfield G, Lathrop R, Senear D. DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions. IEEE/ACM Trans Comput Biol Bioinform. 2007;4:117-25 pubmed
    ..Deformation energy may also have a predictive capacity for the underlying catalytic mechanism of DNA-binding enzymes. ..
  29. Steiner J, Yusa F, Pompe J, Löffelhardt W. Homologous protein import machineries in chloroplasts and cyanelles. Plant J. 2005;44:646-52 pubmed
    ..In chloroplasts, multiple receptors with overlapping and less stringent specificities have evolved, explaining the efficient heterologous import of native precursors from C. paradoxa...
  30. Zhang X, Yang G, Liu Y, Yu W, Pan K, Li R, et al. Induction of programmed cell death in aging Prorocentrum donghaiense cells as was evidenced preliminarily by the identification of associated transcripts. Acta Biol Hung. 2006;57:473-83 pubmed
    ..donghaiense. The identified included also calmodulin and protein phosphatase, two proteins involved in diverse cell processes including PCD by binding to or modifying others. ..
  31. Neupert J, Karcher D, Bock R. Generation of Chlamydomonas strains that efficiently express nuclear transgenes. Plant J. 2009;57:1140-50 pubmed publisher
  32. Labadorf A, Link A, Rogers M, Thomas J, Reddy A, Ben Hur A. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics. 2010;11:114 pubmed publisher
  33. Bittner L, Payri C, Couloux A, Cruaud C, de Reviers B, Rousseau F. Molecular phylogeny of the Dictyotales and their position within the Phaeophyceae, based on nuclear, plastid and mitochondrial DNA sequence data. Mol Phylogenet Evol. 2008;49:211-26 pubmed publisher
    ..Zonaria stipitata clustered with the Spatoglossum species; since this is consistent with its morphological features, the new combination Spatoglossum stipitatum is proposed accordingly. ..
  34. Alverson A. Molecular systematics and the diatom species. Protist. 2008;159:339-53 pubmed publisher
  35. Ma Y, Jakowitsch J, Deusch O, Henze K, Martin W, Löffelhardt W. Transketolase from Cyanophora paradoxa: in vitro import into cyanelles and pea chloroplasts and a complex history of a gene often, but not always, transferred in the context of secondary endosymbiosis. J Eukaryot Microbiol. 2009;56:568-76 pubmed publisher
    ..By contrast, transketolase genes in some eukaryotes with secondary plastids of red algal origin, such as Thalassiosira pseudonana, have retained the pre-existing transketolase gene germane to their secondary host...
  36. Williams B, Slamovits C, Patron N, Fast N, Keeling P. A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc Natl Acad Sci U S A. 2005;102:10936-41 pubmed
    ..These findings also point to serious practical difficulties in studying expression in compacted genomes, because many techniques, such as arrays or serial analysis of gene expression will be misleading...
  37. Verbruggen H, Maggs C, Saunders G, Le Gall L, Yoon H, De Clerck O. Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evol Biol. 2010;10:16 pubmed publisher
    ..Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research. ..
  38. Fernández Benéitez M, Ortiz Santaliestra M, Lizana M, Diéguez Uribeondo J. Saprolegnia diclina: another species responsible for the emergent disease 'Saprolegnia infections' in amphibians. FEMS Microbiol Lett. 2008;279:23-9 pubmed publisher
    ..This will be important in order to design strategies to prevent the impact and spread of species (or strains) pathogenic to amphibians...
  39. Chevalier B, Sussman D, Otis C, Noël A, Turmel M, Lemieux C, et al. Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry. 2004;43:14015-26 pubmed
    ..Failure to occupy the shared metal site, as observed in the presence of calcium or when the metal-binding side chain from the LAGLIDADG motif (Asp 20) is mutated to asparagine, prevents cleavage by the enzyme. ..
  40. Ylla I, Borrego C, Romani A, Sabater S. Availability of glucose and light modulates the structure and function of a microbial biofilm. FEMS Microbiol Ecol. 2009;69:27-42 pubmed publisher
  41. Fraser C, Spencer H, Waters J. Glacial oceanographic contrasts explain phylogeography of Australian bull kelp. Mol Ecol. 2009;18:2287-96 pubmed publisher
    ..The deep east-west divergence seems consistent with earlier reports of morphological differences between 'western' and 'eastern' D. potatorum, and it seems likely that these forms represent reproductively isolated species...
  42. Vardi A, Thamatrakoln K, Bidle K, Falkowski P. Diatom genomes come of age. Genome Biol. 2008;9:245 pubmed publisher
    ..The results of two published genome sequences from marine diatoms provide basic insights into how these remarkable organisms evolved to become one of the most successful groups of eukaryotic algae in the contemporary ocean. ..
  43. Andreakis N, Procaccini G, Maggs C, Kooistra W. Phylogeography of the invasive seaweed Asparagopsis (Bonnemaisoniales, Rhodophyta) reveals cryptic diversity. Mol Ecol. 2007;16:2285-99 pubmed
    ..taxiformis diverged into two main cryptic species (1 + 2 and 3 + 4) about 3.2-5.5 million years ago (Ma), and that the separation of the mitochondrial lineages 1 and 2 occurred 1-2.3 Ma. ..
  44. Ueki N, Nishii I. Idaten is a new cold-inducible transposon of Volvox carteri that can be used for tagging developmentally important genes. Genetics. 2008;180:1343-53 pubmed publisher
    ..This clearly indicates that Idaten is a potentially powerful alternative to Jordan for tagging developmentally important genes in Volvox...
  45. Brouard J, Otis C, Lemieux C, Turmel M. Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer. BMC Genomics. 2008;9:290 pubmed publisher
    ..Our unprecedented finding of int and dpoB in this cpDNA provides a clear example that novel genes were acquired by the chloroplast genome through horizontal transfers, possibly from a mitochondrial genome donor. ..
  46. Nyati S, Beck A, Honegger R. Fine structure and phylogeny of green algal photobionts in the microfilamentous genus Psoroglaena (Verrucariaceae, lichen-forming ascomycetes). Plant Biol (Stuttg). 2007;9:390-9 pubmed
  47. Turmel M, Gagnon M, O Kelly C, Otis C, Lemieux C. The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids. Mol Biol Evol. 2009;26:631-48 pubmed publisher
  48. Iglesias Rodriguez M, Probert I, Batley J. Microsatellite cross-amplification in coccolithophores: application in population diversity studies. Hereditas. 2006;143:99-102 pubmed
    ..The microsatellite markers used in this study may be applied to other coccolithophorid species for population analysis, eliminating the time-consuming, costly development of microsatellite markers for other coccolithophorid species. ..
  49. Mower J, Bonen L. Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae. BMC Evol Biol. 2009;9:265 pubmed publisher
    ..These results illustrate the power of comparative sequencing to identify novel genomic features. ..
  50. Sorhannus U, Ortiz J, Wolf M, Fox M. Microevolution and speciation in Thalassiosira weissflogii (Bacillariophyta). Protist. 2010;161:237-49 pubmed publisher
    ..Three hypotheses which potentially can explain the genetic diversification/similarity between the Atlantic T. weissflogii samples and the isolate obtained off the coast of California were proposed and discussed. ..
  51. Otsuka S, Abe Y, Fukui R, Nishiyama M, Sendoo K. Presence of previously undescribed bacterial taxa in non-axenic Chlorella cultures. J Gen Appl Microbiol. 2008;54:187-93 pubmed
    ..They may have been 'as-yet-uncultured' but in practice unintentionally been cultured in microalgal cultures. They could serve as good bioresources in various fields of biological and ecological studies. ..
  52. Gonzalez Ballester D, Camargo A, Fernandez E. Ammonium transporter genes in Chlamydomonas: the nitrate-specific regulatory gene Nit2 is involved in Amt1;1 expression. Plant Mol Biol. 2004;56:863-78 pubmed
    ..Thus, NIT2 would have a dual role on gene expression: the well-known positive one on nitrate assimilation and a novel negative one on Amt1;1 regulation...
  53. Paul B, Steciow M. Achlya spiralis, a new aquatic oomycete with bent oogonial stalks, isolated from the Burgundian region of France. FEMS Microbiol Lett. 2008;284:120-5 pubmed publisher
    ..The internal transcribed spacer (ITS) region of its rRNA is comprised of 671 bases. The taxonomic description of this new species, its comparison with related oomycetes and the sequence of the ITS region of its rRNA are discussed here...