A protocol for a single-cell PCR of diatoms from fixed samples: method validation using Ditylum brightwellii (T. West) Grunow

References

• Alverson , A. J. , Jansen , R. K. and Theriot , E. C. 2007 . Bridging the rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms . Molecular Phylogenetic Evolution , 45 : 193 – 210 .
   PubMed Web of Science ®Google Scholar
• Amato , A. , Kooistra , W. H.C.F. and Ghiron , J. H.L. 2007 . Reproductive isolation among sympatric cryptic species in marine diatoms . Protist , 158 : 193 – 207 .
   PubMed Web of Science ®Google Scholar
• Armbrust , E. , Berges , J. A. and Bowler , C. 2004 . The genome of Thalassiosira pseudonana: ecology, evolution, and metabolism . Science , 306 : 79 – 86 .
   PubMed Web of Science ®Google Scholar
• Auinger , B. M. , Pfandl , K. and Boenigk , J. 2008 . An improved methodology for the identification of protists and microalgae from plankton samples preserved in Lugol's iodine solution: combining microscopic analysis with single cell PCR . Applied Environmental Microbiology , 74 : 2505 – 2510 .
   PubMed Web of Science ®Google Scholar
• Bhattacharya , D. 1996 . Analysis of the distribution of bootstrap tree lengths using the maximum parsimony method . Molecular Phylogenetic Evolution , 6 : 339 – 350 .
   PubMed Web of Science ®Google Scholar
• Bowler , C. , Allen , A. E. and Bagger , J. H. 2008 . The Phaeodactylum genome reveals the evolutionary history of diatom genomes . Nature , 456 : 239 – 244 .
   PubMed Web of Science ®Google Scholar
• Daugbjerg , N. and Andersen , R. A. 1997 . A molecular phylogeny of the heterokont algae based on analyses of chloroplast-encoded rbcL sequence data . Journal of Phycology , 33 : 1031 – 1041 .
   Web of Science ®Google Scholar
• Edvardsen , B. , Shalchian-Tabrizi , K. , Jakobsen , K. S. , Medlin , L. K. , Dahl , E. , Brubak , S. and Paasche , E. 2003 . Genetic variability and molecular phylogeny of Dinophysis species (Dinophyceae) from Norwegian waters inferred from single cell analyses of rDNA . Journal of Phycology , 39 : 395 – 408 .
   Web of Science ®Google Scholar
• Godhe , A. , Anderson , D. M. and Rehnstam-Holm , A. S. 2002 . PCR amplification of microalgal DNA for sequencing and species identification: studies on fixatives and algal growth stages . Harmful Algae , 1 : 375 – 382 .
   Google Scholar
• Hahn , S. , Zhong , X. Y. , Troeger , C. , Burgemeister , R. , Gloning , K. and Holzgreve , W. 2000 . Current applications of single-cell PCR . Cellular and Molecular Life Sciences , 57 : 96 – 105 .
   PubMed Web of Science ®Google Scholar
• Hall , T. A. 1999 . BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT . Nucleic Acids Symposium Series , 41 : 95 – 98 .
   Google Scholar
• Henegariu , O. , Heerema , N. A. , Dlouhy , S. R. , Vance , G. H. and Vogt , P. H. 1997 . Multiplex PCR: critical parameters and step-by-step protocol . Biological Techniques , 23 : 504 – 511 .
   PubMed Web of Science ®Google Scholar
• Li , D. , Zhang , L. L. , Ju , X. L. , Hou , H. S. , Shi , Q. and Shen , B. J. 2007 . Study of single cell PCR for HLA typing . Zhonghua Xue Ye Xue Za Zhi , 28 : 308 – 311 .
   PubMedGoogle Scholar
• Lovejoy , C. , Massana , R. and Pedros-Alio , C. 2006 . Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas . Applied and Environmental Microbiology , 72 : 3085 – 3095 .
   PubMed Web of Science ®Google Scholar
• Lundholm , N. , Moestrup , Ø. , Hasle , G. R. and Hoef-Emden , K. 2003 . A study of the Pseudo-nitzschia pseudodelicatissima/cuspidata complex (Bacillariophyceae): what is P. pseudodelicatissima? . Journal of Phycology , 39 : 797 – 813 .
   Web of Science ®Google Scholar
• Kaczmarska , I. , Beaton , M. , Benoit , A. C. and Medlin , L. K. 2006 . Molecular phylogeny of selected members of the Order Thalassiosirales (Bacillariophyta) and evolution of the fultoportula . Journal of Phycology , 42 : 121 – 138 .
   Web of Science ®Google Scholar
• Kaczmarska , I. , Reid , C. , Martin , J. L. and Moniz , M. B.J. 2008 . Morphological, biological and molecular characteristics of Pseudo-nitzschia delicatissima from the Canadian Maritimes . Canadian Journal of Botany , 86 : 763 – 772 .
   Google Scholar
• Ki , J. S. , Jang , G. Y. and Han , M. S. 2005 . Integrated method for single-cell DNA extraction, PCR amplification, and sequencing of ribosomal DNA from harmful dinoflagellates Cochlodinium polykrikoides and Alexandrium catenella . Marine Biotechnology , 6 : 587 – 593 .
   Web of Science ®Google Scholar
• Malmgren , H. , Sahlén , S. , Inzunza , J. , Aho , M. , Rosenlund , B. , Fridström , M. , Hovatta , O. , Ährlund-Richter , L. , Nordenskjöld , M. and Blennow , E. 2002 . Single cell CGH analysis reveals a high degree of mosaicism in human embryos from patients with balanced structural chromosome aberrations . Molecular Human Reproduction , 8 : 502 – 510 .
   PubMed Web of Science ®Google Scholar
• Mann , D. G. 1994 . “ The origins of shape and form in diatoms: the interplay between morphogenetic studies and systematics ” . In Shape and form in plants and fungi , Edited by: Ingram , D. S. and Hudson , A. 17 – 38 . London : The Linnean Society of London .
   Google Scholar
• Mann , D. G. 1999 . The species concept in diatoms . Phycologia , 38 : 437 – 495 .
   Web of Science ®Google Scholar
• Moniz , M. B.J. and Kaczmarska , I. 2009 . Barcoding diatoms: is there a good marker? . Molecular Ecology Resources , 9 : 65 – 74 .
   PubMed Web of Science ®Google Scholar
• Moniz , M. B.J. and Kaczmarska , I. 2010 . Barcoding of diatoms: nuclear encoded ITS revisited . Protist , 161 : 7 – 34 .
   PubMed Web of Science ®Google Scholar
• Orsini , L. , Procaccini , G. , Sarno , D. and Montresor , M. 2004 . Multiple rDNA ITS-types within the diatom Pseudo-nitzschia delicatissima (Bacillariophyceae) and their relative abundance across a spring bloom in the Gulf of Naples . Marine Ecology Progress Series , 271 : 87 – 98 .
   Web of Science ®Google Scholar
• Quijano-Scheggia , S. I. , Garces , E. , Lundholm , N. , Moestrup , Ø. and Camp , J. 2009 . Morphology, physiology, molecular phylogeny and sexual compatibility of the cryptic Pseudo-nitzschia delicatissima complex (Bacillariophyta), including the description of P. arenysensis sp. nov . Phycologia , 48 : 492 – 509 .
   Web of Science ®Google Scholar
• Ruiz Sebastián , C. and O'Ryan , C. 2001 . Single-cell sequencing of dinoflagellate (Dinophyceae) nuclear ribosomal genes . Molecular Ecology Notes , 1 : 329 – 331 .
   Google Scholar
• Rynearson , T. A. , Newton , J. A. and Armbrust , E. V. 2006 . Spring bloom development, genetic variation, and population succession in the planktonic diatom Ditylum brightwellii . Limnology and Oceanography , 5 : 1249 – 1261 .
   Google Scholar
• Rynearson , T. A. , Lin , E. O. and Armbrust , E. V. 2009 . Metapopulation structure in the planktonic diatom Ditylum brightwellii (Bacillariophyceae) . Protist , 160 : 111 – 121 .
   PubMed Web of Science ®Google Scholar
• Savin , M. C. , Martin , J. L. , Legresley , M. , Giewat , M. and Rooney-Varga , J. 2004 . Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods . Microbial Ecology , 48 : 51 – 65 .
   PubMed Web of Science ®Google Scholar
• Sherbakova , T. A. , Rubtsov , N. B. , Likhoshway , Y. V. and Grachev , M. A. 2000 . Combined SEM ultrastructure studies and PCR with individual diatom cells . Diatom Research , 15 : 349 – 354 .
   Web of Science ®Google Scholar
• Takano , Y. and Horigushi , T. 2005 . Acquiring scanning electron microscopical, light microscopical and multiple gene sequence data from a single dinoflagellate cell . Journal of Phycology , 42 : 251 – 256 .
   Web of Science ®Google Scholar
• Thompson , J. D. , Higgins , D. G. and Gibson , T. J. 1994 . CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice . Nucleic Acids Research , 22 : 4673 – 4680 .
   PubMed Web of Science ®Google Scholar
• Tomas , C. R. 1997 . Identifying marine phytoplankton , 858 San Diego : Academic Press .
   Google Scholar
• White , T. J. , Bruns , T. D. , Lee , S. B. and Taylor , J. W. 1990 . “ Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics ” . In PCR protocols: a guide to methods and applications Edited by: Innis , M. A. , Gelfand , D. H. , Sninsky , J. J. and White , T. J. 315 – 322 . San Diego Academic Press
   Google Scholar
• Youn , S. J. , Jung , S. W. and Lee , J. H. 2007 . Morphology and sequence analysis of the marine diatom . Ditylum brightwellii , Direct Submission to GenBank
   Google Scholar
• Zechman , F. M. , Zimmer , E. A. and Theriot , E. 1994 . Use of ribosomal DNA internal transcribed spacers for phylogenetic studies in diatoms . Journal of Phycology , 30 : 507 – 512 .
   Web of Science ®Google Scholar