Identification of north-western Atlantic Porphyra (Bangiaceae, Bangiales) based on sequence variation in nuclear SSU and plastid rbcL genes

Phycologia

Volumn 42, Issue 2, 2003, Pages 109-122

  Klein, Anita S ^a   Mathieson, Arthur C ^a   Neefus, Christopher D ^a   Cain, Danielle F ^a   Taylor, Heather A ^a   Teasdale, Brian W ^a   West, Andrew L ^a   Hehre, Edward J ^a   Brodie, Juliet ^b   Yarish, Charles ^c   Wallace, Aaron L ^a  

^a UNIVERSITY OF NEW HAMPSHIRE   (United States)

^b BATH SPA UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; BANGIACEAE; BANGIALES; CLUPEA HARENGUS; EUKARYOTA; PORPHYRA; PORPHYRA AMPLISSIMA; PORPHYRA BIRDIAE; PORPHYRA DIOICA; PORPHYRA LEUCOSTICTA; PORPHYRA LINEARIS; PORPHYRA MINIATA; PORPHYRA PURPUREA; PORPHYRA SP.; PORPHYRA SUBORBICULATA; PORPHYRA UMBILICALIS; PORPHYRA YEZOENSIS;

EID: 0037656052     PISSN: 00318884     EISSN: None     Source Type: Journal    
DOI: 10.2216/i0031-8884-42-2-109.1     Document Type: Article

References (81)

1. ALTSCHUL S.F., GISH W., MILLER W., MYERS E.W. & LIPMAN D.J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
2. ALTSCHUL S.F., MADDEN T.L., SCHÄFFER A.A., ZHANG J., ZHANG Z., MILLER W. & LIPMAN D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
3. AVISE J.C. 1994. Molecular markers, natural history, and evolution. Chapman and Hall, New York. 499 pp.
4. BIRD C.J. & MCLACHLAN J. 1992. Seaweed flora of the Maritimes. 1. Rhodophyta - the red algae. Biopress, Bristol, UK. 177 pp.
5. BIRD C.J., RICE E.L., MURPHY C.A. & RAGAN M.A. 1992. Phylogenetic relationships in the Gracilariales (Rhodophyta) as determined by 18S rDNA. Phycologia 31: 510-522.
6. BRAVERSTOCK P.R. & MORITZ C. 1996. Project design. In: Molecular systematics (Ed. by D.M. Hillis, C. Moritz & B.K. Mable), pp. 17-28. Sinauer Associates, Sunderland, Massachusetts.
7. BRODIE J. & IRVINE L.M. 1997. A comparison of Porphyra dioica sp. nov. and P. purpurea (Roth) C. Ag. (Rhodophyta: Bangiophycidae) in Europe. Cryptogamie, Algologie 18: 283-297.
8. BRODIE J., HAYES P.K., BARKER G.L. & IRVINE L.M. 1996. Molecular and morphological characters distinguishing two Porphyra species (Rhodophyta: Bangiophycidae). European Journal of Phycology 31: 303-308.
9. BRODIE J., HAYES P.K., BARKER G.L., IRVINE L.M. & BARTSCH I. 1998. A reappraisal of Porphyra and Bangia (Bangophycidae, Rhodophyta) in the northeast Atlantic based on the rbcL-rbcS intergenic spacer. Journal of Phycology 34: 1069-1074.
10. BROOM J.E., JONES W.A., HILL D.F., KNIGHT G.A. & NELSON W.A. 1999. Species recognition in New Zealand Porphyra using 18S rDNA sequencing. Journal of Applied Phycology 11: 421-428.
11. BROOM J.E., NELSON W.A., YARISH C., JONES W.A., AGUILAR ROSAS R. & AGUILAR ROSAS L.E. 2002. A reassessment of the taxonomic status of Porphyra suborbiculata, Porphyra carolinensis and Porphyra lilliputiana (Bangiales, Rhodophyta) based on molecular and morphological data. European Journal of Phycology 37: 227-236.
12. CAIN D.F. 2000. Genetic characterization and phylogenetic analysis of native western North Atlantic Porphyra, using the 18S ribosomal gene. MS thesis. University of New Hamphsire, Durham, New Hampshire. 76 pp.
13. CHOI H.G., KIM M.S., GUIRY M.D. & SAUNDERS G.W. 2001. Phylogenetic relationships of Polysiphonia (Rhodomelaceae, Rhodophyta) and its relatives based on anatomical and nuclear small-subunit rDNA sequence data. Canadian Journal of Botany 799: 1465-1476.
14. COLL J. & COX J. 1977. The genus Porphyra C. Ag. (Rhodophyta, Bangiales) in the American North Atlantic. I. New species from North Carolina. Botanica Marina 20: 155-159.
15. D'AQUILA R.T., BECHTEL L.J., VITELER J.A., ERON J.J., GORCZYCA P. & KAPLIN J.C. 1991. Maximizing sensitivity and specificity of PCR by preamplification heating. Nucleic Acids Research 19: 37-49.
16. DE RIJK P. & DE WACHTER R. 1993. DCSE, an interactive tool for sequence alignment and secondary structure research. Computer Applied Biosciences 9: 735-740.
17. DOYLE J.J. & DOYLE J.L. 1990. Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
18. ENGELS W.R. 1993. Contributing software to the Internet: the Amplify program. Trends in Biochemical Sciences 18: 448-450.
19. FRESHWATER D.W., FREDERICQ S., BUTLER B.S., HOMMERSAND M.H. & CHASE M.W. 1994. A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL. Proceedings of the National Academy of Science of the United States of America 91: 7281-7285.
20. GRIFFITHS C.S. 1997. Correlation of functional domains and rates of nucleotide substitution in cytochrome b. Molecular Phylogenetics and Evolution 7: 352-365.
21. HANISAK M.D. 1998. Seaweed cultivation: global trends. World Aquaculture 29: 18-21.
22. HEHRE E.J. & MATHIESON A.C. 1970. Investigations of New England marine algae II. Composition, seasonal occurrence and reproductive periodicity of the marine Rhodophyceae in New Hampshire. Rhodora 72: 194-239.
23. HEHRE E.J. & MATHIESON A.C. 1993. Porphyra amplissima (Kjellman) Setchell et Hus: new records of an 'arctic' seaweed in southern Maine, New Hampshire, and northern Massachusetts. Rhodora 95: 184-187.
24. HILLIS D.M., MORITZ C., PORTER C.A. & BAKER R.J. 1991. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 251: 308-310.
25. HUMM H.J. 1979. The marine algae of Virginia. Special Papers in Marine Science, number 3. University Press of Virginia, Charlottesville. 263 pp.
26. KAPRAUN D.F. & FRESHWATER D.W. 1987. Karyological studies of five species of Porphyra (Bangiales, Rhodophyta) from the North Atlantic and Mediterranean. Phycologia 26: 82-87.
27. KAPRAUN D.F., HINSON T.K. & LEMUS A.J. 1991. Karyology and cytophotometric estimation of interspecific and intraspecific nuclear DNA variation in four species of Porphyra (Rhodophyta). Phycologia 30: 458-466.
28. KINGSBURY J.M. 1969. The seaweeds of Cape Cod and the islands. Chatham Press, Chatham, Massachusetts. 212 pp.
29. KORNMANN P. 1986. Porphyra yezoensis bei Helgoland - eine entwicklungsgeschichtliche Studie. Helgoländer wissenschaftliche Meeresuntersuchangen 40: 327-342.
30. KORNMANN P. 1994. Life histories of monostromatic Porphyra species as a basis for taxonomy and classification. European Journal of Phycology 29: 69-71.
31. KORNMANN P. & SAHLING P.-H. 1991. The Porphyra species of Helgoland (Bangiales, Rhodophyta). Helgoländer Meeresuntersuchungen 45: 1-38.
32. KUNIMOTO M., KITO H., KAMINISHI Y., MIZUKAMI Y. & MURASE N. 1999a. Molecular divergence of the SSU rRNA gene and internal transcribed spacer 1 in Porphyra yezoensis (Rhodophyta). Journal of Applied Phycology 11: 211-216.
33. KUNIMOTO M., KITO H., YAMAMOTO Y., CHENEY D.P., KAMINISHI Y. & MIZUKAMI Y. 1999b. Discrimination of Porphyra species based on small subunit ribosomal RNA gene sequence. Journal of Applied Phycology 11: 203-209.
34. LEVINE I.R. 1998. Commercial cultivation of Porphyra (nori) in the United States. World Aquaculture 29: 37-38, 45-47.
35. LINDSTROM S.C. & COLE K.M. 1992. Relationships between some North Atlantic and North Pacific species of Porphyra. Canadian Journal of Botany 70: 1355-1363.
36. LINDSTROM S.C. & COLE K.M. 1993. The systematics of Porphyra: character evolution in closely related species. Hydrobiologia 260/261: 151-157.
37. MARSTON M.F. & VILLALARD-BOHNSACK M. 2002. Genetic variability and potential sources of Grateloupia doryphora (Halymeniaceae, Rhodophyta) an invasive species in Rhode Island waters (USA). Journal of Phycology 38: 639-658.
38. MATHIESON A.C. & HEHRE E.J. 1986. A synopsis of New Hampshire seaweeds. Rhodora 88: 1-139.
39. MATHIESON A.C., DAWES C.J. & HEHRE E.J. 1998. Floristic and zonation studies of seaweeds from Mount Desert Island, Maine: an historical comparison. Rhodora 100: 333-379.
40. MCIVOR L., MAGGS C.A., PROVAN J. & STANHOPE M.J. 2001. rbcL sequences reveal multiple cryptic introductions of the Japanese red alga Polysiphonia harveyi. Molecular Ecology 10: 911-919.
41. MITMAN G.G. 1992. Meiosis, blade development and sex determination in Porphyra umbilicalis (L.) J. Agardh from Avonport, Nova Scotia, Canada. PhD thesis. Dalhousie University, Nova Scotia, Canada. 142 pp.
42. MITMAN G.G. & VAN DER MEER J.P. 1994. Meiosis, blade development, and sex determination in Porphyra purpurea (Rhodophyta). Journal of Phycology 30: 147-159.
43. MIZUKAMI Y., KAMINISHI Y., KUNIMOTO M., KOBAYASHI M., MURASE N. & KITO H. 1998. Comparison of partial nucleotide sequences in the exonic region of a small subunit ribosomal RNA gene for discrimination of laver (Porphyra) species and cultivars. Fisheries Science, Tokyo 64: 886-891.
44. MÜLLER K.M., SHEATH R.G., VIS M.L., CREASE T.J. & COLE K.M. 1998. Biogeography and systematics of Bangia (Bangiales, Rhodophyta) based on the Rubisco spacer, rbcL gene and 18S rRNA gene sequences and morphometric analyses. I. North America. Phycologia 37: 195-207.
45. MÜLLER K.M., CANNONE J.J., GUTELL R.R. & SHEATH R.G. 2001. A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta). Molecular Biology and Evolution 18: 1654-1667.
46. MULLIS K.B. & FALOONA F.A. 1987. Specifc synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. In: Recombinant DNA Part F (Ed. by R. Wu), pp. 335-350. Academic Press, San Diego.
47. NEEFUS C.D., MATHIESON A.C., YARISH C., KLEIN A.S., WEST A., TEASDALE B. & HEHRE E.J. 2000. Five cryptic species of Porphyra from the Northwest Atlantic. Journal of Phycology 36, supplement: 73.
48. NELSON W.A., KNIGHT G.A. & HAWKES M.W. 1998. Porphyra lilliputiana sp. nov. (Bangiales. Rhodophyta): a diminutive New Zealand endemic with novel reproductive biology. Phycological Research 46: 57-61.
49. NELSON W.A., BROOM J.E. & FARR T.J. 2001. Four new species of Porphyra (Bangiales, Rhodophyta) from the New Zealand region described using traditional characters and 18S rDNA sequence data. Cryptogamie, Algologie 22: 263-284.
50. OKAYAMA H., CURIEL D.T., BRANTLY M.L., HOLMES M.D. & CRYSTAL R.G. 1989. Rapid, nonradioactive detection of mutations in the human genome by allele-specific amplification. Journal of Laboratory and Clinical Medicine 114: 105-113.
51. OLIVEIRA M.C. & BHATTACHARYA D. 2000. Phylogeny of the Bangiophycidae (Rhodophyta) and the secondary endosymbiotic origin of algal plastids. American Journal of Botany 87: 482-492.
52. OLIVEIRA M.C. & RAGAN M.A. 1994. Variant forms of a group I intron in nuclear small-subunit rRNA genes of the marine red alga. Molecular Biology and Evolution 11: 195-207.
53. OLIVEIRA M.C., KURNIAWAN J., BIRD C.J., RICE E.L., MURPHY C.A., SINGH R.K., GUTELL R.R. & RAGAN M.A. 1995. A preliminary investigation of the order Bangiales (Bangiophycidae, Rhodophyta) based on the sequences of nuclear small-subunit ribosomal RNA genes. Phycological Research 43: 71-79.
54. OLMSTEAD R.G. & PALMER J.D. 1994. Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany 81: 1205-1224.
55. RAGAN M.A., BIRD C.J., RICE E.L., GUTELL R.R., MURPHY C.A. & SINGH R.K. 1994. A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proceedings of the National Academy of Science of the United States of America 91: 7276-7280.
56. REITH M. & MUNHOLLAND J. 1993. A high-resolution gene map of the chloroplast genome of the red alga Porphyra purpurea. Plant Cell 5: 465-475.
57. REITH M. & MUNHOLLAND J. 1995. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Molecular Biology Reporter 13: 333-335.
58. RINTOUL T.L., SHEATH R.G. & VIS M. 1999. Systematics and biogeography of the Compsopogonales (Rhodophyta) with emphasis on the freshwater families in North America. Phycologia 38: 517-525.
59. SAVOLAINEN V.W., CÉNOUD P., SPICHIGER R., MARTINEZ M.D., CRÈVECOEUR M. & MANEN J.F. 1995. The use of herbarium specimens in DNA phylogenetics: evaluation and improvement. Plant Systematics and Evolution 197: 87-98.
60. SCHNEIDER C.W. & SEARLES R.B. 1991. Seaweeds of the southeastern United States. Duke University Press, Durham, North Carolina. 553 pp.
61. SCHNEIDER C.W., SUYEMOTO M.M. & YARISH C. 1979. An annotated checklist of Connecticut seaweeds. State Geological and Natural History Survey, Connecticut Department of Environmental Protection, Hartford, Connecticut. 20 pp.
62. SEARS J.R. [Ed.] 2002. NEAS keys to benthic marine algae of the northeastern coast of North America from Long Island Sound to the Strait of Belle Isle, ed. 2. Contribution No. 2. Northeast Algal Society, Dartmouth, Massachusetts. 161 pp.
63. SEELANAN T., SCHNABEL A. & WENDEL J.F. 1997. Congruence and consensus in the cotton tribe (Malvaceae). Systematic Botany 22: 259-290.
64. SILVA P.C. 1999. Porphyra. Index Nominum Algarum. Web page: http://ucjeps.berkeley.edu/rlmoe/porphyra.html (revised 20 December 1999). University Herbarium. University of California, Berkeley.
65. SILVA P.C., BASSON P.W. & MOE R.L. 1996. Catalogue of the benthic marine algae of the Indian Ocean. University of California Publications in Botany 79: 1-1259.
66. SOUTH G.R. & TITTLEY I.A. 1986. Checklist and distributional index of the benthic algae of the North Atlantic Ocean. Huntsman Marine Laboratory, St Andrews, New Brunswick, Canada, and British Museum (Natural History), London. 76 pp.
67. STILLER J.W. & WAALAND J.R. 1993. Molecular analysis reveals cryptic diversity in Porphyra (Rhodophyta). Journal of Phycology 29: 506-517.
68. SWOFFORD D.L. 1998. PAUP*. Phylogenetic analysis using parsimony (* and other methods), version 4. Sinauer Associates, Sunderland, Massachusetts.
69. SWOFFORD D.L., OLSEN G.J., WADDELL P.J. & HILLIS D.M. 1997. Phylogenetic inference. In: Molecular systematics (Ed. by D.M. Hillis, C. Moritz & B.K. Mable), pp. 407-515. Sinauer Associates, Sunderland, Massachusetts.
70. TAMURA K. & NEI M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10:512-526.
71. TAYLOR W.R. 1957. Marine algae of the northeastern coast of North America. University of Michigan Press, Ann Arbor. 509 pp.
72. TEASDALE B.W., WEST A.L., TAYLOR H. & KLEIN A.S. 2002. A simple restriction fragment length polymorphism (RFLP) assay to discriminate common Porphyra (Bangiophyceae, Rhodophyta) taxa from the northwest Atlantic. Journal of Applied Phycology 14: 293-298.
73. VILLALARD-BOHNSACK M. 1995. Illustrated key to the seaweeds of New England. Rhode Island Natural History Survey, Kingston, Rhode Island. 146 pp.
74. VILLALARD-BOHNSACK M. 1998. Non-indigenous benthic algal species introduced to the northeastern coast of North America. In: NEAS keys to the benthic marine algae of the northeastern coast of North America from Long Island Sound to the Strait of Belle Isle (Ed. by J. Sears), pp. 130-131. Contribution No. 1. Northeast Algal Society, Dartmouth, Massachusetts.
75. WILKES R.J., YARISH C. & MITMAN G.G. 1999. Observations on the chromosome numbers of Porphyra (Bangiales, Rhodophyta) populations from Long Island Sound to the Canadian Maritimes. Algae 14: 219-222.
76. WU D.Y., UGOZZLI L., PAL B.K. & WALLACE R.B. 1989. Allele-specific enzymatic amplification of beta globin genomic DNA for diagnosis of sickle cell anemia. Proceedings of the National Academy of Science of the United States of America 86: 2757-2760.
77. YAMAZAKI S., KITADE Y., MARUYAMA T. & SAGA N. 1996. Phylogenetic position of Porphyra yezoensis based on the 18S rDNA sequence. Journal of Marine Biotechnology 4: 230-232.
78. YARISH C., WILKES R., CHOPIN T., FEI X.G., MATHIESON A.C., KLEIN A.S., NEEFUS C.D., MITMAN G.G. & LEVINE I. 1998. Domestication of indigenous Porphyra (nori) species for commercial cultivation in northeast America. World Aquaculture 29: 26-30.
79. YARISH C., CHOPIN T., WILKES R., MATHIESON A.C., FEI X.G. & LU S. 1999. Domestication of nori for northeast America: the Asian experience. Bulletin of the Aquaculture Association of Canada 99: 11-17.
80. YOSHIDA T. 1997. The history and future prospects of systematics of Bangiaceae, Rhodophyta. Natural History Research, Special Issue 3: 1-4.
81. YOSHIDA T., NOTOYA M., KIKUCHI N. & MIYATA M. 1997. Catalogue of species of Porphyra in the world, with special reference to the type locality and bibliography. Natural History Research, Special Issue 3: 5-18.