Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms

Methods in Molecular Biology

Volumn 858, Issue , 2012, Pages 207-222

  Saunders, Gary W ^a   McDevit, Daniel C ^a  

^a UNIVERSITY OF NEW BRUNSWICK   (Canada)

Author keywords

Bacillariophyta; Chlorophyta; COI 5P; DNA barcode; DNA barcoding; LSU; Phaeophyceae; Protist; rbcL 3P; Rhodophyta; tufA

Indexed keywords

ALGAL DNA; CYTOCHROME C OXIDASE; ELONGATION FACTOR TU;

ARTICLE; BIODIVERSITY; BIOGEOGRAPHY; BROWN ALGA; CELL SELECTION; DIATOM; DNA BARCODING; DNA EXTRACTION; DNA PURIFICATION; DNA SEQUENCE; EMBRYOPHYTA; GENOME; GREEN ALGA; MACROALGA; MOLECULAR ECOLOGY; NONHUMAN; PHOTOSYNTHESIS; PLASTID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTIST; RED ALGA; SPECIES IDENTIFICATION; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; PHYLOGENY; SEAWEED;

DIATOMS; DNA BARCODING, TAXONOMIC; DNA, ALGAL; PHOTOSYNTHESIS; PHYLOGENY; POLYMERASE CHAIN REACTION; SEAWEED;

EID: 84871671992     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-591-6_10     Document Type: Article

References (21)

1. Saunders GW (2005) Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Phil Trans R Soc B 360:1879-1888
2. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifi cations through DNA barcodes. Proc R Soc Lond B 270:313-322
3. Hebert PDN, Ratnasingham S, deWaard JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B 270: S96-S99
4. Saunders GW (1993) Gel purifi cation of red algal genomic DNA: an inexpensive and rapid method for the isolation of polymerase chain reaction-friendly DNA. J Phycol 29:251-254
5. Saunders GW, Kraft GT (1995) The phylogenetic affi nities of Notheia anomala (Fucales, Phaeophyceae) as determined from partial small-subunit rRNA gene sequences. Phycologia 34:383-389
6. Ivanova NV, Fazekas AJ, Hebert PDN (2008) Semi-automated, membrane-based protocol for DNA isolation from plants. Plant Mol Biol Rep 26:186-198
7. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fi sh DNA barcoding. Mol Ecol Notes 7:544-548
8. Hamsher SE, Evans KM, Mann DG, Poulícková A, Saunders GW (2011) Barcoding diatoms: exploring alternatives to COI-5P. Protist 162: 405-422
9. Saunders GW, Kucera H (2010) An evaluation of rbc L, tufA , UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae. Crypt Algol 31:487-528
10. Maddison WP, Maddison DR (2003) MacClade, version 4.06. Sinauer, Sunderland
11. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, Kearse M, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2010) Geneious v5.1. http://www.geneious.com
12. Guillou L, Nézan E, Cueff V, Erard-Le Denn E, Cambon-Bonavita MA, Gentien P, Barbier G (2002) Genetic diversity and molecular detection of three toxic dinofl agellate genera ( Alexandrium , Dinophysis , and Karenia ) from French Coasts. Protist 153:223-238
13. McDonald SM, Sarno D, Zingone A (2007) Identifying Pseudo-nitzschia in natural samples using genus-specifi c PCR primers and clone libraries. Harmful Algae 6:849-860
14. Saunders GW (2008) A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity.The foliose Dilsea-Neodilsea complex and Weeksia Botany 86:773-789
15. Kucera H, Saunders GW (2008) Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding. Botany 86:1065-1079
16. McDevit DC, Saunders GW (2009) On the utility of DNA barcoding for species differentiation among brown macroalgae (Phaeophyceae) including a novel extraction protocol. Phycol Res 57:131-141
17. Trobajo R, Mann DG, Clavero E, Evans KM, Vanormelingen P, McGregor RC (2011) The use of partial cox 1, rbc L and LSU rDNA sequences for phylogenetics and species identifi cation within the Nitzschia palea species complex (Bacillariophyceae). Eur J Phycol 45: 413-425
18. Harper JT, Saunders GW (2001) The application of sequences of the ribosomal cistron to the systematics and classifi cation of the fl orideophyte red algae (Florideophyceae, Rhodophyta). Cah Biol Mar 42:25-38
19. Harper JT, Saunders GW (2001) Molecular systematics of the Florideophyceae (Rhodophyta) using nuclear large-and small-subunit rDNA sequence data. J Phycol 37:1073-1082
20. Levialdi Ghiron JH, Amato A, Montresor M, Kooistra WH (2008) Plastid inheritance in the planktonic raphid pinnate diatom Pseudonitzschia delicatissima (Bacillariophyceae). Protist 159:91-98
21. Fama P, Wysor B, Kooistra W, Zuccarello GC (2002) Molecular phylogeny of the genus Caulerpa (Caulerpales, Chlorophyta) inferred from chloroplast tufA gene. J Phycol 38: 1040-1050