441
Views
1
CrossRef citations to date
0
Altmetric
Research Article

Two new bacilladnaviruses associated with the diatom Haslea ostrearia

ORCID Icon, ORCID Icon, ORCID Icon, , , , , , , , & show all
Pages 444-453 | Received 28 Aug 2019, Accepted 18 Mar 2020, Published online: 01 Jun 2020

References

  • Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
  • Arsenieff, L., Simon, N., Rigaut-Jalabert, F., Le Gall, F., Chaffron, S., Corre, E., Com, E., Bigeard, E. & Baudoux, A.-C. (2019). First viruses infecting the marine diatom Guinardia delicatula. Frontiers in Microbiology, 9: 3235. doi: 10.3389/fmicb.2018.03235.
  • Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., Lesin, V.M., Nikolenko, S.I., Pham, S., Prjibelski, A.D., Pyshkin, A.V., Sirotkin, A.V., Vyahhi, N., Tesler, G., Alekseyev, M.A. & Pevzner, P.A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19: 455–477.
  • Bettarel, Y., Kan, J., Wang, K., Williamson, K., Cooney, S., Ribblett, S., Chen, F., Wommack, K.E. & Coats D.W. (2005). Isolation and preliminary characterisation of a small nuclear inclusion virus infecting the diatom Chaetoceros cf. gracilis. Aquatic Microbial Ecology, 40: 103–114.
  • Boratyn, G.M., Camacho, C., Cooper, P.S., Coulouris, G., Fong, A., Ma, N., Madden, T.L., Matten, W.T., McGinnis, S.D., Merezhuk, Y., Raytselis, Y., Sayers, E.W., Tao, T., Ye, J. & Zaretskaya, I. (2013). BLAST: a more efficient report with usability improvements. Nucleic Acids Research, 41: W29–W33. doi: 10.1093/nar/gkt282.
  • Capella-Gutiérrez, S., Silla-Martínez, J.M. & Gabaldón, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25: 1972–1973.
  • Chen, S., Huang, T., Zhou, Y., Han, Y. & Gu, J. (2017). AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics, 18: 80. doi: 10.1186/s12859-017-1469-3.
  • Crooks, G.E., Hon, G., Chandonia, J.M. & Brenner, S.E. (2004). WebLogo: a sequence logo generator. Genome Research, 14: 1188–1190.
  • Darling, A.E., Mau, B. & Perna, N.T. (2010). ProgressiveMauve: multiple genome alignment with gene gain, loss, and rearrangement. PLoS ONE, 5(6): e11147.
  • Davidovich, N.A., Mouget, J.-L. & Gaudin, P. (2009). Heterothallism in the pennate diatom Haslea ostrearia (Bacillariophyta). European Journal Phycology, 44: 251–261.
  • Dayaram, A., Goldstien, S., Argüello-Astorga, G.R., Zawar-Reza, P., Gomez, C., Harding, J.S. & Varsani, A. (2015). Diverse small circular DNA viruses circulating amongst estuarine molluscs. Infection, Genetics and Evolution, 31: 284–295.
  • Dimmic, M.W., Rest, J.S., Mindell, D.P. & Goldstein, R.A. (2002). rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of Molecular Evolution, 55: 65–73.
  • Doyle, J.J. & Doyle, J.L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12: 13–15.
  • Eissler, Y., Wang, K., Chen, F., Wommack, E. & Coats, W. (2009). Ultrastructural characterization of the lytic cycle of an intranuclear virus infecting the diatom Chaetoceros cf. wighamii (bacillariophyceae) from Chesapeake Bay, USA. Journal of Phycology, 45: 787–797.
  • Falaise, C., Cormier, P., Tremblay, R., Audet, C., Deschênes, J.S., Turcotte, F., François, C., Seger, A., Hallegraeff, G., Lindquist, N., Sirjacobs, D., Gobert, S., Lejeune, P., Demoulin, V. & Mouget, J.L. (2019a). Harmful or harmless: biological effects of marennine on marine organisms. Aquatic Toxicology, 209: 13–25.
  • Falaise, C., James, A., Travers, M.-A., Zanella, M., Badawi, M. & Mouget, J.-L. (2019b). Complex relationships between the blue pigment marennine and marine bacteria of the genus Vibrio. Marine Drugs, 17: 160. doi: 10.3390/md17030160.
  • Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R.D. & Bairoch, A. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31: 3784–3788.
  • Gastineau, R., Davidovich, N.A., Bardeau, J.-F., Caruso, A., Leignel, V., Hardivillier, Y., Jacquette, B., Davidovich, O., Rincé, Y., Gaudin, P., Cox, E. & Mouget, J.-L. (2012a). Haslea karadagensis (Bacillariophyta): a second blue diatom, recorded from the Black Sea and producing a novel blue pigment. European Journal of Phycology, 47: 469–479.
  • Gastineau, R., Pouvreau, J.-B., Hellio, C., Morançais, M., Fleurence, J., Gaudin, P., Bourgougnon, N. & Mouget, J.-L. (2012b). Biological activities of purified marennine, the blue pigment responsible for the greening of oysters. Journal of Agricultural and Food Chemistry, 60: 3599–3605.
  • Gastineau, R., Leignel, V., Jacquette, B., Bendahmane, D., Hardivillier, Y., Wulff, A., Gaudin P., Kaczmarska, I., Davidovich, N.A. & Mouget, J.-L. (2013). Inheritance of mitochondrial DNA in the pennate diatom Haslea ostrearia (Naviculaceae) during auxosporulation suggests a uniparental transmission. Protist, 164: 340–351.
  • Gastineau, R., Davidovich, N.A., Hansen, G., Rines, J., Wulff, A., Kaczmarska, I., Ehrman, J., Hermann, D., Maumus, F., Hardivillier, Y., Leignel, V., Jacquette, B., Méléder, V., Hallegraeff, G., Yallop, M., Perkins, R., Cadoret, J.-P., Saint-Jean, B., Carrier, G. & Mouget, J.-L. (2014a). Haslea ostrearia-like diatoms: biodiversity out of the blue. Advances in Botanical Research, 71: 441–446.
  • Gastineau, R., Turcotte, F., Pouvreau, J.-B., Morançais, M., Fleurence, J., Windarto, E., Semba Prasetiya, F., Arsad, S., Jaouen, P., Babin, M., Coiffard, L., Couteau, C., Bardeau, J.-F., Jacquette, B., Leignel, V., Hardivillier, Y., Marcotte, I., Bourgougnon, N., Tremblay, R., Deschênes, J.-S., Badawy, H., Pasetto, P., Davidovich, N.A., Hansen, G., Dittmer, J. & Mouget, J.-L. (2014b). Marennine, promising blue pigments from a widespread Haslea diatom species complex. Marine Drugs, 12: 3161–3189.
  • Gastineau, R., Hansen, G., Davidovich, N.A., Davidovich, O., Bardeau, J.-F., Kaczmarska, I., Ehrman, J. M., Leignel, V., Hardivillier, Y., Jacquette, B., Poulin, M., Morançais, M., Fleurence, J. & Mouget, J.-L. (2016). A new blue-pigmented hasleoid diatom, Haslea provincialis, from the Mediterranean Sea. European Journal of Phycology, 51: 156–170.
  • Gordon, D., Abajian, C. & Green, P. (1998). Consed: a graphical tool for sequence finishing. Genome Research, 3: 195–202.
  • Greiner, S., Lehwark, P. & Bock, R. (2019). OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research, 47: W59–W64. doi: 10.1093/nar/gkz238.
  • Guillard, R.R.L. (1975). Culture of phytoplankton for feeding marine invertebrates. In Culture of Marine Invertebrate Animals (Smith, W.L. & Chanley, M.H., editors), 26–60. Plenum Press, New York.
  • Kadono, T., Miyagawa-Yamaguchi, A., Kira, N., Tomaru, Y., Okami, T., Yoshimatsu, T., Hou, L., Ohama, T., Fukunaga, K., Okauchi, M., Yamaguchi, H., Ohnishi, K., Falciatore, A. & Adachi, M. (2015). Characterization of marine diatom-infecting virus promoters in the model diatom Phaeodactylum tricornutum. Scientific Reports, 5: 18708. http://doi.org/10.1038/srep18708.
  • Katoh, K. & Standley, D.M. (2016). A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics, 32: 1933–1942.
  • Kazlauskas, D., Dayaram, A., Kraberger, S., Goldstien, S., Varsani, A. & Krupovic, M. (2017). Evolutionary history of ssDNA bacilladnaviruses features horizontal acquisition of the capsid gene from ssRNA nodaviruses. Virology, 504: 114–121.
  • Kimura, K. & Tomaru, Y. (2013). Isolation and characterization of a single-stranded DNA virus infecting the marine diatom Chaetoceros sp. strain SS628-11 isolated from Western Japan. PLoS ONE 8(12): e82013. doi: 10.1371/journal.pone.0082013.
  • McDaniel, L.D., Rosario, K., Breitbart, M. & Paul, J.H. (2014). Comparative metagenomics: natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences. Environmental Microbiology, 16: 570–585.
  • Miranda, J.A., Culley, A.I., Schvarcz, C.R. & Steward, G.F. (2016). RNA viruses as major contributors to Antarctic virioplankton. Environmental Microbiology, 18: 3714–3727.
  • Mouget, J.-L., Gastineau, R., Davidovich, O., Gaudin, P. & Davidovich, N.A. (2009). Light is a key factor in triggering sexual reproduction in the pennate diatom Haslea ostrearia. FEMS Microbiology Ecology, 69: 194–201.
  • Nagasaki, K., Tomaru, Y., Katanozaka, N., Shirai, Y., Nishida, K., Itakura, S. & Yamaguchi, M. (2004). Isolation and characterization of a novel single-stranded RNA virus infecting the bloom-forming diatom Rhizosolenia setigera. Applied and Environmental Microbiology, 70: 704–711.
  • Nagasaki, K., Tomaru, Y., Takao, Y., Nishida, K., Shirai, Y., Suzuki, H. & Nagumo, T. (2005). Previously unknown virus infects marine diatom. Applied and Environmental Microbiology, 71: 3528–3535.
  • Neuville, D. & Daste, P. (1975). Observations préliminaires concernant l’auxosporulation chez la diatomée Navicula ostrearia (Gaillon) Bory en culture in vitro. Comptes Rendus de l’Académie des Sciences de Paris, 281: 1753–1756.
  • Neuville, D. & Daste, P. (1979). Observations concernant les phases de l’auxosporulation chez la diatomée Navicula ostrearia (Gaillon) Bory en culture in vitro. Comptes Rendus de l’Académie des Sciences de Paris, 288: 1496–1498.
  • Perkins, R.G., Mouget, J.-L., Lefebvre, S. & Lavaud, J. (2006). Light response curve methodology and possible implications in the application of chlorophyll fluorescence to benthic diatoms. Marine Biology, 149: 703–712.
  • Poulin, M., Méléder, V. & Mouget, J.-L. (2019). Typification of the first recognized blue pigmented diatom, Haslea ostrearia (Bacillariophyceae). Plant Ecology and Evolution, 152: 402–408.
  • Pouvreau, J.B., Housson, E., Le Tallec, L., Morançais, M., Rincé, Y., Fleurence, J. & Pondaven, P. (2007). Growth inhibition of several marine diatom species induced by the shading effect and allelopathic activity of marennine, a blue-green polyphenolic pigment of the diatom Haslea ostrearia (Gaillon/Bory) Simonsen. Journal of Experimental Marine Biology and Ecology, 352: 212–225.
  • Pouvreau, J.B., Morançais, M., Taran, F., Rosa, P., Dufossé, L., Guérard, F., Pin, S., Fleurence, J. & Pondaven, P. (2008). Antioxidant and free radical scavenging properties of marennine, a blue-green polyphenolic pigment from the diatom Haslea ostrearia (Gaillon/Bory) Simonsen responsible for the natural greening of cultured oysters. Journal of Agricultural and Food Chemistry, 56: 6278–6286.
  • Prasetiya, F.S., Comeau, L.A., Gastineau, R., Decottignies, P., Cognie, B., Morançais, M., Turcotte, F., Mouget, J.-L. & Tremblay, R. (2017). Effect of marennine produced by the blue diatom Haslea ostrearia on behavioral, physiological and biochemical traits of juvenile Mytilus edulis and Crassostrea virginica. Aquaculture, 467: 138–148.
  • Prasetiya, F., Gastineau, R., Poulin, M., Lemieux, C., Turmel, M., Syakti, A., Hardivillier, Y., Widowati, I., Risjani, Y., Iskandar, I., Subroto, T., Falaise, C., Arsad, S., Safitri, I., Mouget, J.-L. & Leignel, V. (2019). Haslea nusantara (Bacillariophyceae), a new blue diatom from the Java Sea, Indonesia: morphology, biometry and molecular characterization. Plant Ecology and Evolution, 152: 188–202.
  • Rice, P., Longden, I. & Bleasby, A. (2000). EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16: 276–277.
  • Shirai, Y., Tomaru, Y., Takao, Y., Suzuki, H., Nagumo, T. & Nagasaki, K. (2008). Isolation and characterization of a single-stranded RNA virus infecting the marine planktonic diatom Chaetoceros tenuissimus Meunier. Applied and Environmental Microbiology, 74: 4022–4027.
  • Stamatakis, A. (2014). RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30: 1312–1313.
  • Tomaru, Y., Shirai, Y., Suzuki, H., Nagumo, T. & Nagasaki, K. (2008). Isolation and characterization of a new single-stranded DNA virus infecting the cosmopolitan marine diatom Chaetoceros debilis. Aquatic Microbial Ecology, 50: 103–112.
  • Tomaru, Y., Takao, Y., Suzuki, H., Nagumo, T. & Nagasaki, K. (2009). Isolation and characterization of a single-stranded RNA virus infecting the bloom-forming diatom Chaetoceros socialis. Applied and Environmental Microbiology, 75: 2375–2381.
  • Tomaru, Y., Fujii, N., Oda, S., Toyoda, K. & Nagasaki, K. (2011a). Dynamics of diatom viruses on the western coast of Japan. Aquatic Microbial Ecology, 63: 223–230.
  • Tomaru, Y., Shirai, Y., Toyoda, K. & Nagasaki, K. (2011b). Isolation and characterisation of a single- stranded DNA virus infecting the marine planktonic diatom Chaetoceros tenuissimus. Aquatic Microbial Ecology, 64: 175–184.
  • Tomaru, Y., Takao, Y., Suzuki, H., Nagumo, T., Koike, K. & Nagasaki, K. (2011c). Isolation and characterization of a single-stranded DNA virus infecting Chaetoceros lorenzianus Grunow. Applied and Environmental Microbiology, 77: 5285–5293.
  • Tomaru, Y., Toyoda, K., Kimura, K., Hata, N., Yoshida, M. & Nagasaki, K. (2012). First evidence for the existence of pennate diatom viruses. ISME Journal, 6: 1445–1448.
  • Tomaru, Y., Toyoda, K., Kimura, K., Takao, Y., Sakurada, K., Nakayama, N. & Nagasaki, K. (2013). Isolation and characterization of a single-stranded RNA virus that infects the marine planktonic diatom Chaetoceros sp. (SS08-C03). Phycological Research, 61: 27–36.
  • Toyoda, K., Kimura, K., Hata, N., Nakayama, N., Nagasaki, K. & Tomaru, Y. (2012). Isolation and characterization of a single-stranded DNA virus infecting the marine planktonic diatom Chaetoceros sp. (strain TG07-C28). Plankton and Benthos Research, 7: 20–28.
  • Turcotte, F., Mouget, J.-L., Genard, B., Lemarchand, K., Deschênes, J.-S. & Tremblay, R. (2016). Prophylactic effect of Haslea ostrearia culture supernatant containing the pigment marennine to stabilize bivalve hatchery production. Aquatic Living Resources, 29: 401–409.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.