Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Hughey, Jeffery R ^a   Gabrielson, Paul W ^b   Rohmer, Laurence ^c   Tortolani, Jacquie ^a   Silva, Mayra ^a   Miller, Kathy Ann ^d   Young, Joel D ^e   Martell, Craig ^e   Ruediger, Erik ^e  

^a Hartnell College   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e Naval Postgraduate School   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME MAP; GENETICS; LABORATORY DIAGNOSIS; MITOCHONDRIAL GENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENOME; PLASTID GENOME; PROCEDURES; RED ALGA;

BASE SEQUENCE; CHROMOSOME MAPPING; GENOME, MITOCHONDRIAL; GENOME, PLANT; GENOME, PLASTID; MOLECULAR SEQUENCE DATA; RHODOPHYTA; SPECIMEN HANDLING;

EID: 84902109595     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep05113     Document Type: Article

References (47)

1. McNeill, J. et al. International Code of Botanical Nomenclature For Algae, Fungi, and Plants (Melbourne Code): adopted by the Eighteenth International Botanical Congress Melbourne, Australia, July 2011 (Koeltz Scientific Books, 2012).
2. Staats, M. et al. DNA damage in plant herbarium tissue. PLos ONE 6, e28448 (2011).
3. Freshwater, D. W. amp; Rueness, J. Phylogenetic relationships of some European Gelidium (Gelidiales, Rhodophyta) species based on rbcL nucleotide sequence analysis. Phycologia 33, 187-194 (1994).
4. Presting, G. G. Identification of conserved regions in the plastid genome-implications for DNA barcoding and biological function. Can. J. Bot. 84, 1434-1443 (2006).
5. Hebert, P. D. N., Cywinska, A., Ball, S. L. amp; deWaard, J. R. Biological identifications through DNA barcodes. Proc. R. Soc. B. 270, 313-322 (2003).
6. Saunders, G. W. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 360, 1879-1888 (2005).
7. Hughey, J. R., Silva, P. C. amp; Hommersand, M. H. Solving taxonomic and nomenclatural problems in Pacific Gigartinaceae (Rhodophyta) using DNA from type material. J. Phycol. 37, 1091-1109 (2001).
8. Gabrielson, P. W. Molecular sequencing of Northeast Pacific type material reveals two earlier names for Prionitis lyallii, Prionitis jubata and Prionitis sternbergii, with brief comments on Grateloupia versicolor (Halymeniaceae, Rhodophyta). Phycologia 47, 89-97 (2008).
9. Lindstrom, S. C., Hughey, J. R. amp; Martone, P. T. New, resurrected and redefined species of Mastocarpus (Phyllophoraceae, Rhodophyta) from the northeast Pacific. Phycologia 50, 661-683 (2011).
10. Hind, K. R., Gabrielson, P. W., Lindstrom, S. C. amp; Martone, P. T. Misleading morphologies and the importance of sequencing type specimens for resolving coralline taxonomy (Corallinales, Rhodophyta): Pachyarthron cretaceum is Corallina officinalis. J. Phycol. 50, in press (2014).
11. Hughey, J. R. amp; Gabrielson, P. W. Acquiring DNA sequence data from dried archival red algae (Florideophyceae) for the purpose of applying available names to contemporary genetic species: a critical assessment. Botany 90, 1191-1194 (2012).
12. Sutherland, J. E. et al. A new look at an ancient order: generic revision of the Bangiales (Rhodophyta). J. Phycol. 47, 1131-1151 (2011).
13. Krishnamurthy, V. A revision of the species of the algal genus Porphyra occurring on the pacific coast of North America. Pac. Sci. 26, 24-49 (1972).
14. Conway, E., Mumford, T. F. amp; Scagel, R. F. The genus Porphyra in British Columbia and Washington. Syesis 8, 185-244 (1975).
15. Abbott, I. A. amp; Hollenberg, G. J. Marine Algae of California (Stanford University Press, 1976).
16. Lindstrom, S. C. amp; Cole, K. M. An evaluation of species relationships in the Porphyra perforata complex (Bangiales, Rhodophyta) using starch gel electrophoresis. Hydrobiologia 205, 179-183 (1990).
17. Metzker, M. L. Sequencing technologies-the next generation. Nat. Rev. Genet. 11, 31-46 (2010).
18. Schmieder, R. amp; Edwards, R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 6, e17288 (2011).
19. Wang, L. et al. Complete Sequence and Analysis of Plastid Genomes of Two Economically Important Red Algae: Pyropia haitanensis and Pyropia yezoensis. PLoS ONE 8, e65902 (2013).
20. Reith, M. amp; Munholland, J. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Mol. Biol. Rep. 13, 333-335 (1995).
21. Smith, D. R., Hua, J., Lee, R. W. amp; Keeling, P. J. Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture. Mol. Phylogenet. Evol. 65, 339-344 (2012).
22. Glockner, G., Rosenthal, A. amp; Valentin, K. The structure and gene repertoire of an ancient red algal plastid genome. J. Mol. Evol. 51, 382-390 (2000).
23. Kong, F., Sun, P.,Cao, M.,Wang, L.Mao, Y. Complete mitochondrial genome of Pyropia yezoensis: reasserting the revision of genus Porphyra. Mitochondrial DNA doi:10.3109/19401736.2013.803538.
24. Burger, G., Saint-Louis, D., Gray, M. W. amp; Lang, B. F. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae. Plant Cell 11, 1675-1694 (1999).
25. Mao,Y., Zhang, B., Kong, F. Wang, L. The complete mitochondrial genome of Pyropia haitanensis Chang et Zheng. Mitochondrial DNA 23, 344-346 (2012).
26. Hwang,M. S., Kim, S.-O., Ha, D.-S., Lee, J. E. amp; Sang-Rae, L. Complete sequence and genetic features of the mitochondrial genome of Pyropia tenera (Rhodophyta). Plant Biotechnol. Rep. doi: 10.1007/s11816-013-0281-4 (2013).
27. Kucera, H. amp; Saunders, G. W. A survey of Bangiales (Rhodophyta) based on multiple molecular markers reveals cryptic diversity. J. Phycol. 48, 869-882 (2012).
28. Hus, H. T. A. Preliminary notes on west-coast Porphyras. Zoe 5, 61-70 (1900).
29. Conway, E. An examination of the original specimens of Porphyra perforata J. Ag. (Rhodophyceae, Bangiales). Phycologia 13, 173-177 (1974).
30. Conway, E., Mumford, T. F. amp; Scagel, R. F. The genus Porphyra in British Columbia and Washington. Syesis 8, 185-244 (1975).
31. Mumford, T. F. amp; Cole, K. M. Chromosome numbers for fifteen species in the genus Porphyra (Bangiales, Rhodophyta) from the west coast of North America. Phycologia 16, 373-377 (1977).
32. Cole, K. M. in Biology of the Red Algae (eds Cole K. M., Sheath R. G.) 73-101 (Cambridge University Press, 1990).
33. Bebber, D. P. et al. Herbaria are a major frontier for species discovery. Proc. Natl. Acad. Sci. USA. 107, 22169-22171 (2010).
34. Field, D. et al. Open software for biologists: from famine to feast. Nat. Biotechnol. 24, 801-803 (2006).
35. Zerbino, D. R. amp; Birney, E. Velvet: algorithms for de novo short read assembly using de brujin graphs. Genome Res. 18, 821-829 (2008).
36. Namiki, T., Tanaka, H. amp; Sakakibara, Y. Metavelvet: an extension of velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40, 1-12 (2012).
37. Schattner, P., Brooks, A. N. amp; Lowe, T. M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, 686-689 (2005).
38. Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108 (2007).
39. Darling, A. E., Mau, B. amp; Perna, N. T. ProgressiveMauve: multiple genomic alignment with gene gain, loss, and rearrangement. PLoS One 5, e11147 (2010).
40. Katoh, K. amp; Standley, D. M. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. 30, 772-780 (2013).
41. Waterhouse, A. M., Procter, J. B., Martin, D. M. A.Barton,G. J. Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189-1191 (2009).
42. Stamatakis, A. RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Bioinformatics 30, 1312-1313 (2014).
43. Goecks, J., Nekrutenko, A., Taylor, J. amp; The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).
44. Blankenberg, D. et al. Galaxy: a web-based genome analysis tool for experimentalists. Current Protocols in Molecular Biology 89, 19.10.1-19.10.21 (2010).
45. Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451-1455 (2005).
46. Dereeper, A. et al. Phylogeny. fr: robust phylogenetic analysis for the nonspecialist. Nucleic Acids Res. 36, W465-469 (2008).
47. Deng,W. et al.DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques 48, 405-408 (2010).